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Patel R, Menon J, Kumar S, Nóbrega MB, Patel DA, Sakure AA, Vaja MB. Modern day breeding approaches for improvement of castor. Heliyon 2024; 10:e27048. [PMID: 38463846 PMCID: PMC10920369 DOI: 10.1016/j.heliyon.2024.e27048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 02/12/2024] [Accepted: 02/22/2024] [Indexed: 03/12/2024] Open
Abstract
Castor (Ricinus communis L.) is an industrially important oil producing crop belongs to Euphorbiaceae family. Castor oil has unique chemical properties make it industrially important crop. It is a member of monotypic genus even though it has ample amount of variability. Using this variability, conventionally many varieties and hybrids have been developed. But, like other crops, the modern and unconventional methods of crop improvement has not fully explored in castor. This article discusses the use of polyploidy induction, distant/wide hybridization and mutation breeding as tools for generating variety. Modern approaches accelerate the speed of crop breeding as an alternative tool. To achieve this goal, molecular markers are employed in breeding to capture the genetic variability through molecular analysis and population structuring. Allele mining is used to trace the evolution of alleles, identify new haplotypes and produce allele specific markers for use in marker aided selection using Genome wide association studies (GWAS) and quantitative trait loci (QTL) mapping. Plant genetic transformation is a rapid and effective mode of castor improvement is also discussed here. The efforts towards developing stable regeneration protocol provide a wide range of utility like embryo rescue in distant crosses, development of somaclonal variation, haploid development using anther culture and callus development for stable genetic transformation has reviewed in this article. Omics has provided intuitions to the molecular mechanisms of (a)biotic stress management in castor along with dissected out the possible genes for improving the yield. Relating genes to traits offers additional scientific inevitability leading to enhancement and sympathetic mechanisms of yield improvement and several stress tolerance.
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Affiliation(s)
- Rumit Patel
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand, 388110, India
- Department of Genetics & Plant Breeding, B. A. College of Agriculture, Anand Agricultural University, Anand, 388110, India
| | - Juned Menon
- Department of Genetics & Plant Breeding, B. A. College of Agriculture, Anand Agricultural University, Anand, 388110, India
| | - Sushil Kumar
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand, 388110, India
| | - Márcia B.M. Nóbrega
- Embrapa Algodão, Rua Oswaldo Cruz, nº 1.143, Centenário, CEP 58428-095, Campina Grande, PB, Brazil
| | - Dipak A. Patel
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand, 388110, India
| | - Amar A. Sakure
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand, 388110, India
| | - Mahesh B. Vaja
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand, 388110, India
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Yu A, Zhou Z, Chen Y, Sun J, Li P, Gu X, Liu A. Functional Genome Analyses Reveal the Molecular Basis of Oil Accumulation in Developing Seeds of Castor Beans. Int J Mol Sci 2023; 25:92. [PMID: 38203263 PMCID: PMC10778879 DOI: 10.3390/ijms25010092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Castor (Ricinus communis L.) seeds produce abundant ricinoleic acid during seed maturation, which is important for plant development and human demands. Ricinoleic acid, as a unique hydroxy fatty acid (HFA), possesses a distinct bond structure that could be used as a substitute for fossil fuels. Here, we identified all homologous genes related to glycolysis, hydroxy fatty acid biosynthesis, and triacylglycerol (TAG) accumulation in castor seeds. Furthermore, we investigated their expression patterns globally during five seed development stages. We characterized a total of 66 genes involved in the glycolysis pathway, with the majority exhibiting higher expression levels during the early stage of castor bean seed development. This metabolic process provided abundant acetyl-CoA for fatty acid (FA) biosynthesis. Subsequently, we identified 82 genes involved in the processes of de novo FA biosynthesis and TAG assembly, with the majority exhibiting high expression levels during the middle or late stages. In addition, we examined the expression patterns of the transcription factors involved in carbohydrate and oil metabolism. For instance, RcMYB73 and RcERF72 exhibited high expression levels during the early stage, whereas RcWRI1, RcABI3, and RcbZIP67 showed relatively higher expression levels during the middle and late stages, indicating their crucial roles in seed development and oil accumulation. Our study suggests that the high HFA production in castor seeds is attributed to the interaction of multiple genes from sugar transportation to lipid droplet packaging. Therefore, this research comprehensively characterizes all the genes related to glycolysis, fatty acid biosynthesis, and triacylglycerol (TAG) accumulation in the castor and provides novel insight into exploring the genetic mechanisms underlying seed oil accumulation in the endosperm of castor beans.
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Affiliation(s)
| | | | | | | | | | | | - Aizhong Liu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China; (A.Y.); (Z.Z.); (Y.C.); (J.S.); (P.L.); (X.G.)
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3
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Jardim-Messeder D, Cassol D, Souza-Vieira Y, Ehlers Loureiro M, Girke T, Boroni M, Lopes Corrêa R, Coelho A, Sachetto-Martins G. Genome-wide identification of core components of ABA signaling and transcriptome analysis reveals gene circuits involved in castor bean (Ricinus communis L.) response to drought. Gene 2023; 883:147668. [PMID: 37500024 DOI: 10.1016/j.gene.2023.147668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 07/06/2023] [Accepted: 07/24/2023] [Indexed: 07/29/2023]
Abstract
Castor bean (Ricinus communis L.) can withstand long periods of water deficit and high temperatures, and therefore has been recognized as a drought-resistant plant species, allowing the study of gene networks involved in drought response and tolerance. The identification of genes networks related to drought response in this plant may yield important information in the characterization of molecular mechanisms correlating changes in the gene expression with the physiological adaptation processes. In this context, gene families related to abscisic acid (ABA) signaling play a crucial role in developmental and environmental adaptation processes of plants to drought stress. However, the families that function as the core components of ABA signaling, as well as genes networks related to drought response, are not well understood in castor bean. In this study 7 RcPYL, 63 RcPP2C, and 6 RcSnRK2 genes were identified in castor bean genome, which was further supported by chromosomal distribution, gene structure, evolutionary relationships, and conserved motif analyses. The castor bean general expression profile was investigated by RNAseq in root and leaf tissues in response to drought stress. These analyses allowed the identification of genes differentially expressed, including genes from the ABA signaling core, genes related to photosynthesis, cell wall, energy transduction, antioxidant response, and transcription factors. These analyses provide new insights into the core components of ABA signaling in castor bean, allow the identification of several molecular responses associated with the high physiological adaptation of castor bean to drought stress, and contribute to the identification of candidate genes for genetic improvement.
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Affiliation(s)
- Douglas Jardim-Messeder
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Daniela Cassol
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; Institute for Integrative Genome Biology, Genomics Building, University of California, Riverside, CA 92521, USA
| | - Ygor Souza-Vieira
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Thomas Girke
- Institute for Integrative Genome Biology, Genomics Building, University of California, Riverside, CA 92521, USA
| | - Mariana Boroni
- Bioinformatics and Computational Laboratory, Instituto Nacional de Câncer José Alencar Gomes da Silva, Rio de Janeiro, Brazil
| | - Régis Lopes Corrêa
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ana Coelho
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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Zhou Y, Huang X, Hu T, Chen S, Wang Y, Shi X, Yin M, Li R, Wang J, Jia X. Genome-Wide Analysis of Glycerol-3-Phosphate Acyltransferase (GPAT) Family in Perilla frutescens and Functional Characterization of PfGPAT9 Crucial for Biosynthesis of Storage Oils Rich in High-Value Lipids. Int J Mol Sci 2023; 24:15106. [PMID: 37894786 PMCID: PMC10606570 DOI: 10.3390/ijms242015106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/02/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
Glycerol-3-phosphate acyltransferase (GPAT) catalyzes the first step in triacylglycerol (TAG) biosynthesis. However, GPAT members and their functions remain poorly understood in Perilla frutescens, a special edible-medicinal plant with its seed oil rich in polyunsaturated fatty acids (mostly α-linolenic acid, ALA). Here, 14 PfGPATs were identified from the P. frutescens genome and classified into three distinct groups according to their phylogenetic relationships. These 14 PfGPAT genes were distributed unevenly across 11 chromosomes. PfGPAT members within the same subfamily had highly conserved gene structures and four signature functional domains, despite considerable variations detected in these conserved motifs between groups. RNA-seq and RT-qPCR combined with dynamic analysis of oil and FA profiles during seed development indicated that PfGPAT9 may play a crucial role in the biosynthesis and accumulation of seed oil and PUFAs. Ex vivo enzymatic assay using the yeast expression system evidenced that PfGPAT9 had a strong GPAT enzyme activity crucial for TAG assembly and also a high substrate preference for oleic acid (OA, C18:1) and ALA (C18:3). Heterogeneous expression of PfGPAT9 significantly increased total oil and UFA (mostly C18:1 and C18:3) levels in both the seeds and leaves of the transgenic tobacco plants. Moreover, these transgenic tobacco lines exhibited no significant negative effect on other agronomic traits, including plant growth and seed germination rate, as well as other morphological and developmental properties. Collectively, our findings provide important insights into understanding PfGPAT functions, demonstrating that PfGPAT9 is the desirable target in metabolic engineering for increasing storage oil enriched with valuable FA profiles in oilseed crops.
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Affiliation(s)
- Yali Zhou
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Jinzhong 030801, China; (Y.Z.); (Y.W.); (X.J.)
| | - Xusheng Huang
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Jinzhong 030801, China; (Y.Z.); (Y.W.); (X.J.)
| | - Ting Hu
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Jinzhong 030801, China; (Y.Z.); (Y.W.); (X.J.)
| | - Shuwei Chen
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Jinzhong 030801, China; (Y.Z.); (Y.W.); (X.J.)
| | - Yao Wang
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Jinzhong 030801, China; (Y.Z.); (Y.W.); (X.J.)
| | - Xianfei Shi
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Jinzhong 030801, China; (Y.Z.); (Y.W.); (X.J.)
| | - Miao Yin
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Jinzhong 030801, China; (Y.Z.); (Y.W.); (X.J.)
| | - Runzhi Li
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Jinzhong 030801, China; (Y.Z.); (Y.W.); (X.J.)
| | - Jiping Wang
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Jinzhong 030801, China; (Y.Z.); (Y.W.); (X.J.)
| | - Xiaoyun Jia
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Jinzhong 030801, China; (Y.Z.); (Y.W.); (X.J.)
- College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, China
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Ascorbate-Glutathione Cycle Genes Families in Euphorbiaceae: Characterization and Evolutionary Analysis. BIOLOGY 2022; 12:biology12010019. [PMID: 36671712 PMCID: PMC9855080 DOI: 10.3390/biology12010019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Ascorbate peroxidase (APX), Monodehydroascorbate Reductase (MDAR), Dehydroascorbate Reductase (DHAR) and Glutathione Reductase (GR) enzymes participate in the ascorbate-glutathione cycle, which exerts a central role in the antioxidant metabolism in plants. Despite the importance of this antioxidant system in different signal transduction networks related to development and response to environmental stresses, the pathway has not yet been comprehensively characterized in many crop plants. Among different eudicotyledons, the Euphorbiaceae family is particularly diverse with some species highly tolerant to drought. Here the APX, MDAR, DHAR, and GR genes in Ricinus communis, Jatropha curcas, Manihot esculenta, and Hevea brasiliensis were identified and characterized. The comprehensive phylogenetic and genomic analyses allowed the classification of the genes into different classes, equivalent to cytosolic, peroxisomal, chloroplastic, and mitochondrial enzymes, and revealed the duplication events that contribute to the expansion of these families within plant genomes. Due to the high drought stress tolerance of Ricinus communis, the expression patterns of ascorbate-glutathione cycle genes in response to drought were also analyzed in leaves and roots, indicating a differential expression during the stress. Altogether, these data contributed to the characterization of the expression pattern and evolutionary analysis of these genes, filling the gap in the proposed functions of core components of the antioxidant mechanism during stress response in an economically relevant group of plants.
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Identification and Functional Characterization of the RcFAH12 Promoter from Castor Bean in Arabidopsis thaliana. SEPARATIONS 2022. [DOI: 10.3390/separations10010002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Castor (Ricinus communis L.) seed oil is the commercial source of ricinoleate, a valuable raw material used in many industries. Oleoyl-12-hydroxylase (RcFAH12) is a key enzyme in the biosynthesis of ricinoleate, accumulating nearly 90% of the triacylglycerol in castor seeds. Little is known about the transcriptional regulation of RcFAH12. We used rapid amplification of cDNA 5′ ends (5′RACE) to locate the transcription start site (TSS) of RcFAH12, and the sequence of a 2605 bp region, −2506~+99, surrounding the TSS was cloned. We then investigated these regions to promote β-glucuronidase (GUS) expression in transgenic Arabidopsis by the progressive 5′ and 3′ deletions strategies. The GUS staining showed that the GUS accumulation varied in tissues under the control of different deleted fragments of RcFAH12. In addition, the GUS expression driven by the RcFAH12 promoter markedly accumulated in transgenic seeds, which indicated that RcFAH12 might play an important role in the biosynthesis of ricinoleic acid. This study will lay a potential foundation for developing a tissue-specific promoter in oil-seed crops.
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Lunn D, Wallis JG, Browse J. A multigene approach secures hydroxy fatty acid production in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2875-2888. [PMID: 35560203 DOI: 10.1093/jxb/erab533] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/02/2021] [Indexed: 06/15/2023]
Abstract
A central goal of green chemistry is to produce industrially useful fatty acids in oilseed crops. Although genes encoding suitable fatty acid-modifying enzymes are available from more than a dozen wild species, progress has been limited because expression of these enzymes in transgenic plants produces only low yields of the desired products. For example, fatty acid hydroxylase 12 (FAH12) from castor (Ricinus communis) produces only 17% hydroxy fatty acids (HFAs) when expressed in Arabidopsis (Arabidopsis thaliana), compared with 90% HFAs in castor seeds. The transgenic plants also have reduced oil content and seed vigor. Here, we review experiments that have provided for steady increased HFA accumulation and oil content. This research has led to exciting new discoveries of enzymes and regulatory processes in the pathways of both seed oil synthesis and lipid metabolism in other parts of the plant. Recent investigations have revealed that HFA-accumulating seeds are unable to rapidly mobilize HFA-containing triacylglycerol (TAG) storage lipid after germination to provide carbon and energy for seedling development, resulting in reduced seedling establishment. These findings present a new opportunity to investigate a different, key area of lipid metabolism-the pathways of TAG lipolysis and β-oxidation in germinating seedlings.
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Affiliation(s)
- Daniel Lunn
- Institute of Biology Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | - James G Wallis
- Institute of Biology Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | - John Browse
- Institute of Biology Chemistry, Washington State University, Pullman, WA 99164-6340, USA
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Duan Q, Li GR, Qu YP, Yin DX, Zhang CL, Chen YS. Genome-Wide Identification, Evolution and Expression Analysis of the Glutathione S-Transferase Supergene Family in Euphorbiaceae. FRONTIERS IN PLANT SCIENCE 2022; 13:808279. [PMID: 35360301 PMCID: PMC8963715 DOI: 10.3389/fpls.2022.808279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
Euphorbiaceae, a family of plants mainly grown in the tropics and subtropics, is also widely distributed all over the world and is well known for being rich in rubber, oil, medicinal materials, starch, wood and other economically important plant products. Glutathione S-transferases (GSTs) constitute a family of proteins encoded by a large supergene family and are widely expressed in animals, bacteria, fungi and plants, but with few reports of them in Euphorbiaceae plants. These proteins participate in and regulate the detoxification and oxidative stress response of heterogeneous organisms, resistance to stress, growth and development, signal transduction and other related processes. In this study, we identified and analyzed the whole genomes of four species of Euphorbiaceae, namely Ricinus communis, Jatropha curcas, Hevea brasiliensis, and Manihot esculenta, which have high economic and practical value. A total of 244 GST genes were identified. Based on their sequence characteristics and conserved domain types, the GST supergene family in Euphorbiaceae was classified into 10 subfamilies. The GST supergene families of Euphorbiaceae and Arabidopsis have been found to be highly conserved in evolution, and tandem repeats and translocations in these genes have made the greatest contributions to gene amplification here and have experienced strong purification selection. An evolutionary analysis showed that Euphorbiaceae GST genes have also evolved into new subtribes (GSTO, EF1BG, MAPEG), which may play a specific role in Euphorbiaceae. An analysis of expression patterns of the GST supergene family in Euphorbiaceae revealed the functions of these GSTs in different tissues, including resistance to stress and participation in herbicide detoxification. In addition, an interaction analysis was performed to determine the GST gene regulatory mechanism. The results of this study have laid a foundation for further analysis of the functions of the GST supergene family in Euphorbiaceae, especially in stress and herbicide detoxification. The results have also provided new ideas for the study of the regulatory mechanism of the GST supergene family, and have provided a reference for follow-up genetics and breeding work.
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Affiliation(s)
- Qiang Duan
- College of Life Sciences and Food Engineering, Inner Mongolia Minzu University, Tongliao, China
- Key Laboratory of Castor Breeding of the State Ethnic Affairs Commission, Tongliao, China
- Inner Mongolia Industrial Engineering Research Center of Universities for Castor, Tongliao, China
- Inner Mongolia Key Laboratory of Castor Breeding, Tongliao, China
- Inner Mongolia Collaborative Innovation Center for Castor Industry, Tongliao, China
- Inner Mongolia Engineering Research Center of Industrial Technology Innovation of Castor, Tongliao, China
| | - Guo-Rui Li
- College of Life Sciences and Food Engineering, Inner Mongolia Minzu University, Tongliao, China
- Key Laboratory of Castor Breeding of the State Ethnic Affairs Commission, Tongliao, China
- Inner Mongolia Industrial Engineering Research Center of Universities for Castor, Tongliao, China
- Inner Mongolia Key Laboratory of Castor Breeding, Tongliao, China
- Inner Mongolia Collaborative Innovation Center for Castor Industry, Tongliao, China
- Inner Mongolia Engineering Research Center of Industrial Technology Innovation of Castor, Tongliao, China
- Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, China
| | - Yi-Peng Qu
- Key Laboratory of Castor Breeding of the State Ethnic Affairs Commission, Tongliao, China
- Inner Mongolia Industrial Engineering Research Center of Universities for Castor, Tongliao, China
- Inner Mongolia Key Laboratory of Castor Breeding, Tongliao, China
- Inner Mongolia Collaborative Innovation Center for Castor Industry, Tongliao, China
- Inner Mongolia Engineering Research Center of Industrial Technology Innovation of Castor, Tongliao, China
| | - Dong-Xue Yin
- College of Life Sciences and Food Engineering, Inner Mongolia Minzu University, Tongliao, China
- Key Laboratory of Castor Breeding of the State Ethnic Affairs Commission, Tongliao, China
- Inner Mongolia Industrial Engineering Research Center of Universities for Castor, Tongliao, China
- Inner Mongolia Key Laboratory of Castor Breeding, Tongliao, China
- Inner Mongolia Collaborative Innovation Center for Castor Industry, Tongliao, China
- Inner Mongolia Engineering Research Center of Industrial Technology Innovation of Castor, Tongliao, China
| | - Chun-Ling Zhang
- College of Life Sciences and Food Engineering, Inner Mongolia Minzu University, Tongliao, China
- Key Laboratory of Castor Breeding of the State Ethnic Affairs Commission, Tongliao, China
- Inner Mongolia Industrial Engineering Research Center of Universities for Castor, Tongliao, China
- Inner Mongolia Key Laboratory of Castor Breeding, Tongliao, China
- Inner Mongolia Collaborative Innovation Center for Castor Industry, Tongliao, China
- Inner Mongolia Engineering Research Center of Industrial Technology Innovation of Castor, Tongliao, China
| | - Yong-Sheng Chen
- College of Life Sciences and Food Engineering, Inner Mongolia Minzu University, Tongliao, China
- Key Laboratory of Castor Breeding of the State Ethnic Affairs Commission, Tongliao, China
- Inner Mongolia Industrial Engineering Research Center of Universities for Castor, Tongliao, China
- Inner Mongolia Key Laboratory of Castor Breeding, Tongliao, China
- Inner Mongolia Collaborative Innovation Center for Castor Industry, Tongliao, China
- Inner Mongolia Engineering Research Center of Industrial Technology Innovation of Castor, Tongliao, China
- Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, China
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Han B, Wu D, Zhang Y, Li DZ, Xu W, Liu A. Epigenetic regulation of seed-specific gene expression by DNA methylation valleys in castor bean. BMC Biol 2022; 20:57. [PMID: 35227267 PMCID: PMC8886767 DOI: 10.1186/s12915-022-01259-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 02/18/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Understanding the processes governing angiosperm seed growth and development is essential both for fundamental plant biology and for agronomic purposes. Master regulators of angiosperm seed development are expressed in a seed-specific manner. However, it is unclear how this seed specificity of transcription is established. In some vertebrates, DNA methylation valleys (DMVs) are highly conserved and strongly associated with key developmental genes, but comparable studies in plants are limited to Arabidopsis and soybean. Castor bean (Ricinus communis) is a valuable model system for the study of seed biology in dicots and source of economically important castor oil. Unlike other dicots such as Arabidopsis and soybean, castor bean seeds have a relatively large and persistent endosperm throughout seed development, representing substantial structural differences in mature seeds. Here, we performed an integrated analysis of RNA-seq, whole-genome bisulfite sequencing, and ChIP-seq for various histone marks in the castor bean. RESULTS We present a gene expression atlas covering 16 representative tissues and identified 1162 seed-specific genes in castor bean (Ricinus communis), a valuable model for the study of seed biology in dicots. Upon whole-genome DNA methylation analyses, we detected 32,567 DMVs across five tissues, covering ~33% of the castor bean genome. These DMVs are highly hypomethylated during development and conserved across plant species. We found that DMVs have the potential to activate transcription, especially that of tissue-specific genes. Focusing on seed development, we found that many key developmental regulators of seed/endosperm development, including AGL61, AGL62, LEC1, LEC2, ABI3, and WRI1, were located within DMVs. ChIP-seq for five histone modifications in leaves and seeds clearly showed that the vast majority of histone modification peaks were enriched within DMVs, and their remodeling within DMVs has a critical role in the regulation of seed-specific gene expression. Importantly, further experiment analysis revealed that distal DMVs may act as cis-regulatory elements, like enhancers, to activate downstream gene expression. CONCLUSIONS Our results point to the importance of DMVs and special distal DMVs behaving like enhancers, in the regulation of seed-specific genes, via the reprogramming of histone modifications within DMVs. Furthermore, these results provide a comprehensive understanding of the epigenetic regulator roles in seed development in castor bean and other important crops.
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Affiliation(s)
- Bing Han
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Di Wu
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanyu Zhang
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Wei Xu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
| | - Aizhong Liu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China.
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10
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Wang WB, Ao T, Zhang YY, Wu D, Xu W, Han B, Liu AZ. Genome-wide analysis of the B3 transcription factors reveals that RcABI3/VP1 subfamily plays important roles in seed development and oil storage in castor bean ( Ricinus communis). PLANT DIVERSITY 2022; 44:201-212. [PMID: 35505987 PMCID: PMC9043308 DOI: 10.1016/j.pld.2021.06.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/19/2021] [Accepted: 06/22/2021] [Indexed: 06/14/2023]
Abstract
The B3 transcription factors (TFs) in plants play vital roles in numerous biological processes. Although B3 genes have been broadly identified in many plants, little is known about their potential functions in mediating seed development and material accumulation. Castor bean (Ricinus communis) is a non-edible oilseed crop considered an ideal model system for seed biology research. Here, we identified a total of 61 B3 genes in the castor bean genome, which can be classified into five subfamilies, including ABI3/VP1, HSI, ARF, RAV and REM. The expression profiles revealed that RcABI3/VP1 subfamily genes are significantly up-regulated in the middle and later stages of seed development, indicating that these genes may be associated with the accumulation of storage oils. Furthermore, through yeast one-hybrid and tobacco transient expression assays, we detected that ABI3/VP1 subfamily member RcLEC2 directly regulates the transcription of RcOleosin2, which encodes an oil-body structural protein. This finding suggests that RcLEC2, as a seed-specific TF, may be involved in the regulation of storage materials accumulation. This study provides novel insights into the potential roles and molecular basis of B3 family proteins in seed development and material accumulation.
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Affiliation(s)
- Wen-Bo Wang
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 100049, China
- Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650204, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Tao Ao
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Science, Mengla, 666303, China
| | - Yan-Yu Zhang
- Northwest A&F University, Yangling, 712100, China
| | - Di Wu
- Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650204, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei Xu
- Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650204, China
| | - Bing Han
- Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650204, China
| | - Ai-Zhong Liu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China (Ministry of Education), Southwest Forestry University, Kunming, 650224, China
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11
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Shi R, Bai H, Li B, Liu C, Ying Z, Xiong Z, Wang W. Combined Transcriptome and Lipidomic Analyses of Lipid Biosynthesis in Macadamia ternifolia Nuts. Life (Basel) 2021; 11:1431. [PMID: 34947962 PMCID: PMC8707767 DOI: 10.3390/life11121431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/07/2021] [Accepted: 12/15/2021] [Indexed: 11/17/2022] Open
Abstract
Macadamia nuts are considered a high-quality oil crop worldwide. To date, the lipid diversity and the genetic factors that mediate storage lipid biosynthesis in Macadamia ternifolia are poorly known. Here, we performed a comprehensive transcriptomic and lipidomic data analysis to understand the mechanism of lipid biosynthesis by using young, medium-aged, and mature fruit kernels. Our lipidomic analysis showed that the M. ternifolia kernel was a rich source of unsaturated fatty acids. Moreover, different species of triacylglycerols, diacylglycerol, ceramides, phosphatidylethanolamine, and phosphatidic acid had altered accumulations during the developmental stages. The transcriptome analysis revealed a large percentage of differently expressed genes during the different stages of macadamia growth. Most of the genes with significant differential expression performed functional activity of oxidoreductase and were enriched in the secondary metabolite pathway. The integration of lipidomic and transcriptomic data allowed for the identification of glycerol-3-phosphate acyltransferase, diacylglycerol kinase, phosphatidylinositols, nonspecific phospholipase C, pyruvate kinase 2, 3-ketoacyl-acyl carrier protein reductase, and linoleate 9S-lipoxygenase as putative candidate genes involved in lipid biosynthesis, storage, and oil quality. Our study found comprehensive datasets of lipidomic and transcriptomic changes in the developing kernel of M. ternifolia. In addition, the identification of candidate genes provides essential prerequisites to understand the molecular mechanism of lipid biosynthesis in the kernel of M. ternifolia.
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Affiliation(s)
- Rui Shi
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Landscape Architecture Engineering Research Center of National Forestry and Grassland Administration, Southwest Forestry University, Kunming 650224, China; (R.S.); (C.L.); (Z.Y.)
| | - Haidong Bai
- Lincang Academy of Forestry, Lincang 677009, China;
| | - Biao Li
- Yuxi Sannong Plateau Characteristic Modern Agriculture Co., Ltd., Chengjiang 652599, China;
| | - Can Liu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Landscape Architecture Engineering Research Center of National Forestry and Grassland Administration, Southwest Forestry University, Kunming 650224, China; (R.S.); (C.L.); (Z.Y.)
| | - Zhiping Ying
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Landscape Architecture Engineering Research Center of National Forestry and Grassland Administration, Southwest Forestry University, Kunming 650224, China; (R.S.); (C.L.); (Z.Y.)
| | - Zhi Xiong
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Landscape Architecture Engineering Research Center of National Forestry and Grassland Administration, Southwest Forestry University, Kunming 650224, China; (R.S.); (C.L.); (Z.Y.)
| | - Wenlin Wang
- Guangxi South Subtropical Agricultural Science Research Institute, Longzhou 532415, China
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12
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Milojković-Opsenica DM, Trifković JÐ, Ristivojević PM, Andrić FL. Thin-layer chromatography in the authenticity testing of bee-products. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1188:123068. [PMID: 34864425 DOI: 10.1016/j.jchromb.2021.123068] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 11/17/2021] [Accepted: 11/24/2021] [Indexed: 01/16/2023]
Abstract
Quality control, nutritional value and the monitoring of hazardous residues in honey bee- products have become major topics for both producers and consumers. Due to its potential role in human health, bee-products rich in bioactive compounds are becoming increasingly popular. This review aims to provide an overview of thin-layer chromatography methods used in quality control,authenticity testing and chemical profiling of bee-products in order to help scientists engaged in the field of bee-products chemistry to utilize the advantages of this technique in the detection and elimination of fraudulent practices in bee-product manufacturing. Recently, hyphenation of thin-layer chromatography, image analysis and chemometrics support bee-products analysisbysimultaneousdeterminationofanalytes with different detection principles, identification of individual bioactive compounds as well as structure elucidation of compounds. Highlighted opportunities of thin-layer chromatography could encourage further investigations that would lead to improvements in the detection and elimination of marketing fraudulent practices.
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Affiliation(s)
| | - Jelena Ð Trifković
- University of Belgrade - Faculty of Chemistry, Studentski trg 12-16, 11158 Belgrade, Serbia
| | - Petar M Ristivojević
- University of Belgrade - Faculty of Chemistry, Studentski trg 12-16, 11158 Belgrade, Serbia
| | - Filip Lj Andrić
- University of Belgrade - Faculty of Chemistry, Studentski trg 12-16, 11158 Belgrade, Serbia
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13
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Yu SY, Zhang X, Huang LB, Lyu YP, Zhang Y, Yao ZJ, Zhang XX, Yuan JH, Hu YH. Transcriptomic analysis of α-linolenic acid content and biosynthesis in Paeonia ostii fruits and seeds. BMC Genomics 2021; 22:297. [PMID: 33892636 PMCID: PMC8063412 DOI: 10.1186/s12864-021-07594-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 04/09/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Paeonia ostii is a potentially important oilseed crop because its seed yield is high, and the seeds are rich in α-linolenic acid (ALA). However, the molecular mechanisms underlying ALA biosynthesis during seed kernel, seed testa, and fruit pericarp development in this plant are unclear. We used transcriptome data to address this knowledge gap. RESULTS Gas chromatograph-mass spectrometry indicated that ALA content was highest in the kernel, moderate in the testa, and lowest in the pericarp. Therefore, we used RNA-sequencing to compare ALA synthesis among these three tissues. We identified 227,837 unigenes, with an average length of 755 bp. Of these, 1371 unigenes were associated with lipid metabolism. The fatty acid (FA) biosynthesis and metabolism pathways were significantly enriched during the early stages of oil accumulation in the kernel. ALA biosynthesis was significantly enriched in parallel with increasing ALA content in the testa, but these metabolic pathways were not significantly enriched during pericarp development. By comparing unigene transcription profiles with patterns of ALA accumulation, specific unigenes encoding crucial enzymes and transcription factors (TFs) involved in de novo FA biosynthesis and oil accumulation were identified. Specifically, the bell-shaped expression patterns of genes encoding SAD, FAD2, FAD3, PDCT, PDAT, OLE, CLE, and SLE in the kernel were similar to the patterns of ALA accumulation in this tissue. Genes encoding BCCP, BC, KAS I- III, and FATA were also upregulated during the early stages of oil accumulation in the kernel. In the testa, the upregulation of the genes encoding SAD, FAD2, and FAD3 was followed by a sharp increase in the concentrations of ALA. In contrast, these genes were minimally expressed (and ALA content was low) throughout pericarp development. CONCLUSIONS We used three tissues with high, moderate, and low ALA concentrations as an exemplar system in which to investigate tissue-specific ALA accumulation mechanisms in P. ostii. The genes and TFs identified herein might be useful targets for future studies of ALA accumulation in the tree peony. This study also provides a framework for future studies of FA biosynthesis in other oilseed plants.
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Affiliation(s)
- Shui-Yan Yu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Xiao Zhang
- Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | | | - Yu-Ping Lyu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Ying Zhang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Zu-Jie Yao
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Xiao-Xiao Zhang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Jun-Hui Yuan
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China.
| | - Yong-Hong Hu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China.
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14
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Li D, Wang Q, Xu X, Yu J, Chen Z, Wei B, Wu W. Temporal transcriptome profiling of developing seeds reveals candidate genes involved in oil accumulation in safflower (Carthamus tinctorius L.). BMC PLANT BIOLOGY 2021; 21:181. [PMID: 33858333 PMCID: PMC8051040 DOI: 10.1186/s12870-021-02964-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 04/07/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND The investigation of molecular mechanisms involved in lipid metabolism plays a critical role for the genetic engineering of safflower (Carthamus tinctorius L.) to increase the oil accumulation level or to change the oil composition. Although transcript sequences are currently available for the leaves and flowers of safflower, a wide range scan of temporal transcripts at different stages of seed development has not been conducted for safflower. RESULTS In this study, temporal transcriptome sequencing was executed at 10, 14, 18, and 22 days after flowering (DAF) to uncover the molecular networks concerned in the biosynthesis of unsaturated fatty acids (USFAs). The results revealed that the biosynthesis of fatty acids is a dominant cellular process from 10 to 14 DAF, while degradation mainly happens after 18 DAF. Significant expression changes of two genes, stearoyl-[acyl-carrier-protein] 9-desaturase gene (SAD) from 10 to 14 DAF and oleate desaturase (FAD2-1) from 14 to 18 DAF, were detected at the transcriptomic levels, and the temporal expression patterns revealed by the transcriptomic analysis were confirmed using quantitative real-time PCR experiments. In addition, 13 candidate transcription factors (TFs) involved in regulating the expression level of the FAD2-1 gene were identified. CONCLUSIONS These results create a link between fatty acid biosynthesis and gene expression at different developmental stages of the seeds, provide insight into the underlying lipid metabolism, and meanwhile lay an important foundation for the genetic engineering of safflower varieties. We have identified novel candidate genes, including TFs, that are worthy of further exploration.
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Affiliation(s)
- Dandan Li
- Agronomy College, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
- Agronomy College, Guizhou University, Huaxi, 550025 Guiyang, Guizhou People’s Republic of China
| | - Qing Wang
- Agronomy College, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
| | - Xin Xu
- Agronomy College, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
| | - Jingsheng Yu
- Agronomy College, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
| | - Zhiyu Chen
- Agronomy College, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
| | - Bo Wei
- Agronomy College, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
| | - Wei Wu
- Agronomy College, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
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15
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Wang Z, Kuang J, Han B, Chen S, Liu A. Genomic characterization and expression profiles of stress-associated proteins (SAPs) in castor bean ( Ricinus communis). PLANT DIVERSITY 2021; 43:152-162. [PMID: 33997548 PMCID: PMC8103421 DOI: 10.1016/j.pld.2020.07.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 06/12/2023]
Abstract
Stress-associated proteins (SAPs) are known as response factors to multiple abiotic and biotic stresses in plants. However, the potential physiological and molecular functions of SAPs remain largely unclear. Castor bean (Ricinus communis L.) is one of the most economically valuable non-edible woody oilseed crops, able to be widely cultivated in marginal lands worldwide because of its broad adaptive capacity to soil and climate conditions. Whether SAPs in castor bean plays a key role in adapting diverse soil conditions and stresses remains unknown. In this study, we used the castor bean genome to identify and characterize nine castor bean SAP genes (RcSAP). Structural analysis showed that castor bean SAP gene structures and functional domain types vary greatly, differing in intron number, protein sequence, and functional domain type. Notably, the AN1-C2H2-C2H2 zinc finger domain within RcSAP9 has not been often observed in other plant families. High throughput RNA-seq data showed that castor bean SAP gene profiles varied among different tissues. In addition, castor bean SAP gene expression varied in response to different stresses, including salt, drought, heat, cold and ABA and MeJA, suggesting that the transcriptional regulation of castor bean SAP genes might operate independently of each other, and at least partially independent from ABA and MeJA signal pathways. Cis-element analyses for each castor bean SAP gene showed that no common cis-elements are shared across the nine castor bean SAP genes. Castor bean SAPs were localized to different regions of cells, including the cytoplasm, nucleus, and cytomembrane. This study provides a comprehensive profile of castor bean SAP genes that advances our understanding of their potential physiological and molecular functions in regulating growth and development and their responses to different abiotic stresses.
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Affiliation(s)
- Zaiqing Wang
- College of Life Sciences, Yunnan University, Kunming, 650091, China
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingge Kuang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
| | - Bing Han
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Suiyun Chen
- College of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Aizhong Liu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
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16
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Miray R, Kazaz S, To A, Baud S. Molecular Control of Oil Metabolism in the Endosperm of Seeds. Int J Mol Sci 2021; 22:1621. [PMID: 33562710 PMCID: PMC7915183 DOI: 10.3390/ijms22041621] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/30/2021] [Accepted: 02/02/2021] [Indexed: 12/12/2022] Open
Abstract
In angiosperm seeds, the endosperm develops to varying degrees and accumulates different types of storage compounds remobilized by the seedling during early post-germinative growth. Whereas the molecular mechanisms controlling the metabolism of starch and seed-storage proteins in the endosperm of cereal grains are relatively well characterized, the regulation of oil metabolism in the endosperm of developing and germinating oilseeds has received particular attention only more recently, thanks to the emergence and continuous improvement of analytical techniques allowing the evaluation, within a spatial context, of gene activity on one side, and lipid metabolism on the other side. These studies represent a fundamental step toward the elucidation of the molecular mechanisms governing oil metabolism in this particular tissue. In particular, they highlight the importance of endosperm-specific transcriptional controls for determining original oil compositions usually observed in this tissue. In the light of this research, the biological functions of oils stored in the endosperm of seeds then appear to be more diverse than simply constituting a source of carbon made available for the germinating seedling.
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Affiliation(s)
| | | | | | - Sébastien Baud
- Institut Jean-Pierre Bourgin, INRAE, CNRS, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (R.M.); (S.K.); (A.T.)
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17
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YEBOAH A, YING S, LU J, XIE Y, AMOANIMAA-DEDE H, BOATENG KGA, CHEN M, YIN X. Castor oil (Ricinus communis): a review on the chemical composition and physicochemical properties. FOOD SCIENCE AND TECHNOLOGY 2021. [DOI: 10.1590/fst.19620] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
| | | | | | - Yu XIE
- Guangdong Ocean University, China
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18
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Demski K, Łosiewska A, Jasieniecka-Gazarkiewicz K, Klińska S, Banaś A. Phospholipid:Diacylglycerol Acyltransferase1 Overexpression Delays Senescence and Enhances Post-heat and Cold Exposure Fitness. FRONTIERS IN PLANT SCIENCE 2020; 11:611897. [PMID: 33381143 PMCID: PMC7767865 DOI: 10.3389/fpls.2020.611897] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 11/26/2020] [Indexed: 05/27/2023]
Abstract
In an alternative pathway to acyl-CoA: diacylglycerol acyltransferase (DGAT)-mediated triacylglycerol (TAG) synthesis from diacylglycerol, phospholipid:diacylglycerol acyltransferase (PDAT) utilizes not acyl-CoA but an acyl group from sn-2 position of a phospholipid, to form TAG. The enzyme's activity in vitro matches DGAT's in a number of plant species, however its main function in plants (especially in vegetative tissue) is debatable. In the presented study, we cultivated PDAT1-overexpressing, pdat1 knockout and wild-type lines of Arabidopsis thaliana through their whole lifecycle. PDAT1 overexpression prolonged Arabidopsis lifespan in comparison to wild-type plants, whereas knocking out pdat1 accelerated the plant's senescence. After subjecting the 3-week old seedlings of the studied lines (grown in vitro) to 2-h heat stress (40°C) and then growing them for one more week in standard conditions, the difference in weight between wild-type and PDAT1-overexpressing lines increased in comparison to the difference between plants grown only in optimal conditions. In another experiment all lines exposed to 2-week cold stress experienced loss of pigment, except for PDAT1-overexpressing lines, which green rosettes additionally weighed 4 times more than wild-type. Our results indicate that plants depleted of PDAT1 are more susceptible to cold exposure, while PDAT1 overexpression grants plants a certain heat and cold resilience. Since it was shown, that lysophospholipids may be intertwined with stress response, we decided to also conduct in vitro assays of acyl-CoA:lysophosphatidylcholine acyltransferase (LPCAT) and acylCoA:lysophosphatidylethanolamine acyltransferase (LPEAT) activity in microsomal fractions from the PDAT1-overexpressing Arabidopsis lines in standard conditions. The results show significant increase in LPEAT and LPCAT activity in comparison to wild-type plants. PDAT1-overexpressing lines' rosettes also present twice as high expression of LPCAT2 in comparison to control. The presented study shows how much heightened expression of PDAT1 augments plant condition after stress and extends its lifespan.
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19
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Schmitz J, Hüdig M, Meier D, Linka N, Maurino VG. The genome of Ricinus communis encodes a single glycolate oxidase with different functions in photosynthetic and heterotrophic organs. PLANTA 2020; 252:100. [PMID: 33170407 PMCID: PMC7655567 DOI: 10.1007/s00425-020-03504-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 10/23/2020] [Indexed: 06/11/2023]
Abstract
The biochemical characterization of glycolate oxidase in Ricinus communis hints to different physiological functions of the enzyme depending on the organ in which it is active. Enzymatic activities of the photorespiratory pathway are not restricted to green tissues but are present also in heterotrophic organs. High glycolate oxidase (GOX) activity was detected in the endosperm of Ricinus communis. Phylogenetic analysis of the Ricinus L-2-hydroxy acid oxidase (Rc(L)-2-HAOX) family indicated that Rc(L)-2-HAOX1 to Rc(L)-2-HAOX3 cluster with the group containing streptophyte long-chain 2-hydroxy acid oxidases, whereas Rc(L)-2-HAOX4 clusters with the group containing streptophyte GOX. Rc(L)-2-HAOX4 is the closest relative to the photorespiratory GOX genes of Arabidopsis. We obtained Rc(L)-2-HAOX4 as a recombinant protein and analyze its kinetic properties in comparison to the Arabidopsis photorespiratory GOX. We also analyzed the expression of all Rc(L)-2-HAOXs and conducted metabolite profiling of different Ricinus organs. Phylogenetic analysis indicates that Rc(L)-2-HAOX4 is the only GOX encoded in the Ricinus genome (RcGOX). RcGOX has properties resembling those of the photorespiratory GOX of Arabidopsis. We found that glycolate, the substrate of GOX, is highly abundant in non-green tissues, such as roots, embryo of germinating seeds and dry seeds. We propose that RcGOX fulfills different physiological functions depending on the organ in which it is active. In autotrophic organs it oxidizes glycolate into glyoxylate as part of the photorespiratory pathway. In fast growing heterotrophic organs, it is most probably involved in the production of serine to feed the folate pathway for special demands of those tissues.
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Affiliation(s)
- Jessica Schmitz
- Plant Molecular Physiology and Biotechnology Division, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University, and Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
| | - Meike Hüdig
- Plant Molecular Physiology and Biotechnology Division, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University, and Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
- Molecular Plant Physiology Division, Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Dieter Meier
- Plant Molecular Physiology and Biotechnology Division, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University, and Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
| | - Nicole Linka
- Institute for Plant Biochemistry, Heinrich Heine University, and Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
| | - Veronica G Maurino
- Plant Molecular Physiology and Biotechnology Division, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University, and Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany.
- Molecular Plant Physiology Division, Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, Kirschallee 1, 53115, Bonn, Germany.
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20
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Tian B, Sun M, Jayawardana K, Wu D, Chen G. Characterization of a PLDζ2 Homology Gene from Developing Castor Bean Endosperm. Lipids 2020; 55:537-548. [PMID: 32115716 DOI: 10.1002/lipd.12231] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/18/2020] [Accepted: 02/18/2020] [Indexed: 12/18/2022]
Abstract
Castor oil contains approximately 90% ricinoleic acid (RA) which is stored mainly in the form of tri-ricinoleic acid containing triacylglycerols (TAG). Ricinoleate is synthesized from oleate (18:1n-9) esterified to the sn-2 position of phosphatidylcholine (PtdCho) catalyzed by oleoyl-12-hydroxylase. PtdCho-derived diacylglycerol (DAG) is an important substrate pool for TAG synthesis, and the interconversion between PtdCho and DAG has been shown to play a critical role in channeling hydroxy fatty acids (HFA) to TAG. Although phospholipase D (PLD) has been reported to catalyze the hydrolysis of PtdCho to produce phosphatidic acid which can then be converted to DAG, its potential functions in the channeling of RA from PtdCho to DAG and the assembly of RA on TAG is largely unknown. In the present study, 11 PLD genes were identified from the Castor Bean Genome Database. Gene expression analysis indicated that RcPLD9 is expressed at relatively high levels in developing seeds compared to other plant tissues. Sequence and phylogenetic analyses revealed that RcPLD9 is a homolog of Arabidopsis PLDζ2. Overexpression of RcPLD9 in the Arabidopsis CL7 line producing C18-HFA resulted in RA content reductions in the polar lipid fraction (mainly PtdCho) and mono-HFA-TAG, but increased RA content in di-HFA-TAG. Since part of RA in di-HFA-TAG is derived from HFA-DAG, the results indicated that RcPLD9 facilitates the channeling of RA from PtdCho to DAG for its assembly on TAG in developing seeds.
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Affiliation(s)
- Bo Tian
- CAS Key Laboratory of Tropical Plant Resource and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China
| | - Meijuan Sun
- CAS Key Laboratory of Tropical Plant Resource and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China
| | - Kethmi Jayawardana
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Ding Wu
- Jingdezhen University, Jingdezhen, 333000, China
| | - Guanqun Chen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
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21
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Hernández ML, Lima-Cabello E, Alché JDD, Martínez-Rivas JM, Castro AJ. Lipid Composition and Associated Gene Expression Patterns during Pollen Germination and Pollen Tube Growth in Olive (Olea europaea L.). PLANT & CELL PHYSIOLOGY 2020; 61:1348-1364. [PMID: 32384163 PMCID: PMC7377348 DOI: 10.1093/pcp/pcaa063] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 04/30/2020] [Indexed: 05/23/2023]
Abstract
Pollen lipids are essential for sexual reproduction, but our current knowledge regarding lipid dynamics in growing pollen tubes is still very scarce. Here, we report unique lipid composition and associated gene expression patterns during olive pollen germination. Up to 376 genes involved in the biosynthesis of all lipid classes, except suberin, cutin and lipopolysaccharides, are expressed in olive pollen. The fatty acid profile of olive pollen is markedly different compared with other plant organs. Triacylglycerol (TAG), containing mostly C12-C16 saturated fatty acids, constitutes the bulk of olive pollen lipids. These compounds are partially mobilized, and the released fatty acids enter the β-oxidation pathway to yield acetyl-CoA, which is converted into sugars through the glyoxylate cycle during the course of pollen germination. Our data suggest that fatty acids are synthesized de novo and incorporated into glycerolipids by the 'eukaryotic pathway' in elongating pollen tubes. Phosphatidic acid is synthesized de novo in the endomembrane system during pollen germination and seems to have a central role in pollen tube lipid metabolism. The coordinated action of fatty acid desaturases FAD2-3 and FAD3B might explain the increase in linoleic and alpha-linolenic acids observed in germinating pollen. Continuous synthesis of TAG by the action of diacylglycerol acyltransferase 1 (DGAT1) enzyme, but not phosphoplipid:diacylglycerol acyltransferase (PDAT), also seems plausible. All these data allow for a better understanding of lipid metabolism during the olive reproductive process, which can impact, in the future, on the increase in olive fruit yield and, therefore, olive oil production.
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Affiliation(s)
- M Luisa Hernández
- Department of Biochemistry and Molecular Biology of Plant Products, Instituto de la Grasa (CSIC), Seville 41013, Spain
- Departamento de Bioquímica Vegetal y Biología Molecular, Universidad de Sevilla, Avda. Reina Mercedes s/n, Sevilla 41012, Spain
| | - Elena Lima-Cabello
- Plant Reproductive Biology and Advanced Imaging Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín (CSIC), Granada 18008, Spain
| | - Juan de D Alché
- Plant Reproductive Biology and Advanced Imaging Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín (CSIC), Granada 18008, Spain
| | - José M Martínez-Rivas
- Department of Biochemistry and Molecular Biology of Plant Products, Instituto de la Grasa (CSIC), Seville 41013, Spain
| | - Antonio J Castro
- Plant Reproductive Biology and Advanced Imaging Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín (CSIC), Granada 18008, Spain
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Maghuly F, Deák T, Vierlinger K, Pabinger S, Tafer H, Laimer M. Gene expression profiling identifies pathways involved in seed maturation of Jatropha curcas. BMC Genomics 2020; 21:290. [PMID: 32272887 PMCID: PMC7146973 DOI: 10.1186/s12864-020-6666-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 03/11/2020] [Indexed: 11/10/2022] Open
Abstract
Background Jatropha curcas, a tropical shrub, is a promising biofuel crop, which produces seeds with high content of oil and protein. To better understand the maturation process of J. curcas seeds and to improve its agronomic performance, a two-step approach was performed in six different maturation stages of seeds: 1) generation of the entire transcriptome of J. curcas seeds using 454-Roche sequencing of a cDNA library, 2) comparison of transcriptional expression levels using a custom Agilent 8x60K oligonucleotide microarray. Results A total of 793,875 high-quality reads were assembled into 19,382 unique full-length contigs, of which 13,507 could be annotated with Gene Ontology (GO) terms. Microarray data analysis identified 9111 probes (out of 57,842 probes), which were differentially expressed between the six maturation stages. The expression results were validated for 75 selected transcripts based on expression levels, predicted function, pathway, and length. Result from cluster analyses showed that transcripts associated with fatty acid, flavonoid, and phenylpropanoid biosynthesis were over-represented in the early stages, while those of lipid storage were over-represented in the late stages. Expression analyses of different maturation stages of J. curcas seed showed that most changes in transcript abundance occurred between the two last stages, suggesting that the timing of metabolic pathways during seed maturation in J. curcas occurs in late stages. The co-expression results showed that the hubs (CB5-D, CDR1, TT8, DFR, HVA22) with the highest number of edges, associated with fatty acid and flavonoid biosynthesis, are showing a decrease in their expression during seed maturation. Furthermore, seed development and hormone pathways are significantly well connected. Conclusion The obtained results revealed differentially expressed sequences (DESs) regulating important pathways related to seed maturation, which could contribute to the understanding of the complex regulatory network during seed maturation with the focus on lipid, flavonoid and phenylpropanoid biosynthesis. This study provides detailed information on transcriptional changes during J. curcas seed maturation and provides a starting point for a genomic survey of seed quality traits. The results highlighted specific genes and processes relevant to the molecular mechanisms involved in Jatropha seed maturation. These data can also be utilized regarding other Euphorbiaceae species.
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Affiliation(s)
- Fatemeh Maghuly
- Plant Functional Genomics, Department of Biotechnology, BOKU-VIBT, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.
| | - Tamás Deák
- Department of Viticulture, Szent István University, Villányi út 29-43, 1118 Budapest, Hungary
| | - Klemens Vierlinger
- Center for Health and Bioresources, Molecular Diagnostics, Austrian Institute of Technology (AIT), Giefinggasse 4, 1210, Vienna, Austria
| | - Stephan Pabinger
- Center for Health and Bioresources, Molecular Diagnostics, Austrian Institute of Technology (AIT), Giefinggasse 4, 1210, Vienna, Austria
| | - Hakim Tafer
- Austrian Center of Biological Resources (ACBR), Department of Biotechnology, BOKU-VIBT, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Margit Laimer
- Plant Biotechnology Unit, Department of Biotechnology, BOKU-VIBT, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
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23
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Xu XY, Akbar S, Shrestha P, Venugoban L, Devilla R, Hussain D, Lee J, Rug M, Tian L, Vanhercke T, Singh SP, Li Z, Sharp PJ, Liu Q. A Synergistic Genetic Engineering Strategy Induced Triacylglycerol Accumulation in Potato ( Solanum tuberosum) Leaf. FRONTIERS IN PLANT SCIENCE 2020; 11:215. [PMID: 32210994 PMCID: PMC7069356 DOI: 10.3389/fpls.2020.00215] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 02/12/2020] [Indexed: 05/23/2023]
Abstract
Potato is the 4th largest staple food in the world currently. As a high biomass crop, potato harbors excellent potential to produce energy-rich compounds such as triacylglycerol as a valuable co-product. We have previously reported that transgenic potato tubers overexpressing WRINKLED1, DIACYLGLYCEROL ACYLTRANSFERASE 1, and OLEOSIN genes produced considerable levels of triacylglycerol. In this study, the same genetic engineering strategy was employed on potato leaves. The overexpression of Arabidopsis thaliana WRINKED1 under the transcriptional control of a senescence-inducible promoter together with Arabidopsis thaliana DIACYLGLYCEROL ACYLTRANSFERASE 1 and Sesamum indicum OLEOSIN driven by the Cauliflower Mosaic Virus 35S promoter and small subunit of Rubisco promoter respectively, resulted in an approximately 30- fold enhancement of triacylglycerols in the senescent transgenic potato leaves compared to the wild type. The increase of triacylglycerol in the transgenic potato leaves was accompanied by perturbations of carbohydrate accumulation, apparent in a reduction in starch content and increased total soluble sugars, as well as changes of polar membrane lipids at different developmental stages. Microscopic and biochemical analysis further indicated that triacylglycerols and lipid droplets could not be produced in chloroplasts, despite the increase and enlargement of plastoglobuli at the senescent stage. Possibly enhanced accumulation of fatty acid phytyl esters in the plastoglobuli were reflected in transgenic potato leaves relative to wild type. It is likely that the plastoglobuli may have hijacked some of the carbon as the result of WRINKED1 expression, which could be a potential factor restricting the effective accumulation of triacylglycerols in potato leaves. Increased lipid production was also observed in potato tubers, which may have affected the tuberization to a certain extent. The expression of transgenes in potato leaf not only altered the carbon partitioning in the photosynthetic source tissue, but also the underground sink organs which highly relies on the leaves in development and energy deposition.
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Affiliation(s)
- Xiao-yu Xu
- CSIRO Agriculture and Food, Canberra, ACT, Australia
- Plant Breeding Institute and Sydney Institute of Agriculture, School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, Australia
| | - Sehrish Akbar
- CSIRO Agriculture and Food, Canberra, ACT, Australia
| | | | | | | | - Dawar Hussain
- CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Jiwon Lee
- Center for Advanced Microscopy, The Australian National University, Canberra, ACT, Australia
| | - Melanie Rug
- Center for Advanced Microscopy, The Australian National University, Canberra, ACT, Australia
| | - Lijun Tian
- CSIRO Agriculture and Food, Canberra, ACT, Australia
| | | | | | - Zhongyi Li
- CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Peter J. Sharp
- Plant Breeding Institute and Sydney Institute of Agriculture, School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, Australia
| | - Qing Liu
- CSIRO Agriculture and Food, Canberra, ACT, Australia
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Lin Y, Chen G, Mietkiewska E, Song Z, Caldo KMP, Singer SD, Dyer J, Smith M, McKeon T, Weselake RJ. Castor patatin-like phospholipase A IIIβ facilitates removal of hydroxy fatty acids from phosphatidylcholine in transgenic Arabidopsis seeds. PLANT MOLECULAR BIOLOGY 2019; 101:521-536. [PMID: 31549344 DOI: 10.1007/s11103-019-00915-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 09/04/2019] [Indexed: 06/10/2023]
Abstract
Castor patatin-like phospholipase A IIIβ facilitates the exclusion of hydroxy fatty acids from phosphatidylcholine in developing transgenic Arabidopsis seeds. Hydroxy fatty acids (HFAs) are industrial useful, but their major natural source castor contains toxic components. Although expressing a castor OLEATE 12-HYDROXYLASE in Arabidopsis thaliana leads to the synthesis of HFAs in seeds, a high proportion of the HFAs are retained in phosphatidylcholine (PC). Thus, the liberation of HFA from PC seems to be critical for obtaining HFA-enriched seed oils. Plant phospholipase A (PLA) catalyzes the hydrolysis of PC to release fatty acyl chains that can be subsequently channeled into triacylglycerol (TAG) synthesis or other metabolic pathways. To further our knowledge regarding the function of PLAs from HFA-producing plant species, two class III patatin-like PLA cDNAs (pPLAIIIβ or pPLAIIIδ) from castor or Physaria fendleri were overexpressed in a transgenic line of A. thaliana producing C18-HFA, respectively. Only the overexpression of RcpPLAIIIβ resulted in a significant reduction in seed HFA content with concomitant changes in fatty acid composition. Reductions in HFA content occurred in both PC and TAG indicating that HFAs released from PC were not incorporated into TAG. These results suggest that RcpPLAIIIβ may catalyze the removal of HFAs from PC in the developing seeds synthesizing these unusual fatty acids.
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Affiliation(s)
- Yingyu Lin
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Guanqun Chen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
| | - Elzbieta Mietkiewska
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
- Okanagan Specialty Fruits Inc. (OSF), 410 Downey Road, Saskatoon, SK, S7N 4N1, Canada
| | - Ziliang Song
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Kristian Mark P Caldo
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Stacy D Singer
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, T1J 4B1, Canada
| | - John Dyer
- USDA-ARS, Arid-Land Agricultural Research Center, 21881 North Cardon Lane, Maricopa, AZ, 85138, USA
| | - Mark Smith
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Thomas McKeon
- USDA-ARS, Western Regional Research Center, 800 Buchanan St, Albany, CA, 94710, USA
| | - Randall J Weselake
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
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Deciphering the transcriptomic insight during organogenesis in Castor ( Ricinus communis L.), Jatropha ( Jatropha curcas L.) and Sunflower ( Helianthus annuus L.). 3 Biotech 2019; 9:434. [PMID: 31696039 DOI: 10.1007/s13205-019-1960-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 10/18/2019] [Indexed: 10/25/2022] Open
Abstract
Cultivation of the castor crop is hindered by various factors and one of the approaches for genetic improvement of the crop is through exploitation of biotechnological tools. Response of castor tissues to in vitro culture is poor which necessitated this study on understanding the molecular basis of organogenesis in cultured tissues of castor, through de novo transcriptome analysis and by comparing with jatropha and sunflower having good regeneration ability. Transcriptome profiling analysis was carried out with hypocotyl explants from castor, jatropha and cotyledons from sunflower cultured on MS media supplemented with different concentrations of hormones. Differentially expressed genes during dedifferentiation and organogenic differentiation stages of callus included components of auxin and cytokinin signaling, secondary metabolite synthesis, genes encoding transcription factors, receptor kinases and protein kinases. In castor, many genes involved in auxin biosynthesis and homeostasis like WAT1, vacuolar transporter genes, transcription factors like short root like protein were down-regulated while genes like DELLA were up-regulated accounting for regeneration recalcitrance. Validation of 62 DEGs through qRT-PCR showed a consensus of 77.4% of the genes expressed. Overall study provides set of genes involved in the process of organogenesis in three oilseed crops which forms a basis for understanding and improving the efficiency of plant regeneration and genetic transformation in castor.
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26
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Xu W, Yang T, Qiu L, Chapman MA, Li D, Liu A. Genomic analysis reveals rich genetic variation and potential targets of selection during domestication of castor bean from perennial woody tree to annual semi-woody crop. PLANT DIRECT 2019; 3:e00173. [PMID: 31641699 PMCID: PMC6802463 DOI: 10.1002/pld3.173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 09/05/2019] [Accepted: 09/10/2019] [Indexed: 06/10/2023]
Abstract
Relatively, little is known about the genetic variation of woody trees during domestication. Castor bean (Ricinus communis L. Euphorbiaceae) is a commercially important nonedible annual oilseed crop and differs from its wild progenitors that have a perennial woody habit. Although castor bean is one of the oldest cultivated crops, its domestication origin, genomic variation, and potential targets of selection underlying domestication traits remain unknown. Here, we performed a phylogenetic analysis, which suggests that the wild accessions were distinctively separated from the cultivated accessions. Genome sequencing of three accessions (one each wild, landrace, and cultivar) showed a large number of genetic variants between wild and cultivated castor bean (ZB306 or Hale), and relatively few variants between cultivar ZB306 and Hale. Comparative genome analysis revealed many candidate genes of selection and key pathways potentially involved in the transition from a perennial woody tree to annual crop. Interestingly, among 16 oil-related genes only three showed evidence of selection and the remainder showed low genetic variation at the population level, suggesting strong purifying selection in both the wild and domesticated gene pools. These results extend our understanding of the origin, genomic variation, and domestication, and provide a valuable resource for future gene-trait associations and castor bean breeding.
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Affiliation(s)
- Wei Xu
- Department of Economic Plants and BiotechnologyYunnan Key Laboratory for Wild Plant ResourcesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Tianquan Yang
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Lijun Qiu
- Department of Economic Plants and BiotechnologyYunnan Key Laboratory for Wild Plant ResourcesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Mark A. Chapman
- Biological Sciences and Centre for Underutilised CropsUniversity of SouthamptonSouthamptonUK
| | - De‐Zhu Li
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Aizhong Liu
- Department of Economic Plants and BiotechnologyYunnan Key Laboratory for Wild Plant ResourcesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of ChinaMinistry of EducationSouthwest Forestry UniversityKunmingChina
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Zhou M, Song L, Ye S, Zeng W, Hännien H, Yu W, Suo J, Hu Y, Wu J. New sights into lipid metabolism regulation by low temperature in harvested Torreya grandis nuts. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2019; 99:4226-4234. [PMID: 30790295 DOI: 10.1002/jsfa.9653] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/08/2019] [Accepted: 02/14/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Torreya grandis, a large evergreen coniferous tree with oil-rich nuts, undergoes a crucial ripening stage after harvest that results in oil accumulation, finally giving rise to the nut that is edible in roasted form. To understand lipid metabolism in T. grandis nuts during the post-harvest ripening period, the effects of low temperature on lipid content, fatty acid composition, lipid biosynthesis and degradation were investigated. RESULTS The lipid content increased during ripening at room temperature and a low temperature slowed down this increase. Linoleic acid content increased at low temperature, which was accompanied by an increase in the microsomal oleate desaturase (FAD2) activity and FAD2 expression. Furthermore, a low temperature attenuated lipid peroxidation as indicated by lower contents of malondialdehyde, hydroperoxide and total free fatty acid in T. grandis nuts during the ripening stage, as well as the down-regulation of gene expression of lipid degradation-related enzymes such as phospholipase D and lipoxygenases. CONCLUSION The findings of the present study indicate that a low temperature increased polyunsaturated fatty acid contents by increasing FAD2 biosynthesis and decreasing lipid peroxidation, thereby improving the oil yield in T. grandis nuts during the post-harvest ripening period. © 2019 Society of Chemical Industry.
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Affiliation(s)
| | - Lili Song
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Zhejiang, People's Republic of China
- Sino-Australia Plant Cell Wall Research Centre, School of Forestry and Biotechnology, Zhejiang A&F University, Zhejiang, People's Republic of China
| | - Shan Ye
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Zhejiang, People's Republic of China
| | - Wei Zeng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Zhejiang, People's Republic of China
- Sino-Australia Plant Cell Wall Research Centre, School of Forestry and Biotechnology, Zhejiang A&F University, Zhejiang, People's Republic of China
| | - Heikki Hännien
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Zhejiang, People's Republic of China
| | - Weiwu Yu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Zhejiang, People's Republic of China
| | - Jinwei Suo
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Zhejiang, People's Republic of China
| | - Yuanyuan Hu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Zhejiang, People's Republic of China
| | - Jiasheng Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Zhejiang, People's Republic of China
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Wan X, Liu Q, Dong B, Vibhakaran Pillai S, Huang FH, Singh SP, Zhou XR. Molecular and biochemical analysis of the castor caruncle reveals a set of unique genes involved in oil accumulation in non-seed tissues. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:158. [PMID: 31249621 PMCID: PMC6589891 DOI: 10.1186/s13068-019-1496-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 06/11/2019] [Indexed: 05/30/2023]
Abstract
BACKGROUND With the increasing demand for vegetative oil and the approach of peak seed oil production, it is important to develop new oil production platforms from non-seed tissues. Castor bean (Ricinus communis) is one of the crops for vegetable oil for industrial applications with yield around 1.4 ton oil per hectare produced in seed. The castor caruncle is a non-seed tissue attached to seed. RESULTS Caruncle accumulates up to 40% oil by weight in the form of triacylglycerol (TAG), with a highly contrasting fatty acid composition when compared to the seed oil. Biochemical analysis indicated that the caruncle synthesizes TAGs independent of the seed. Such non-seed tissue has provided an excellent resource for understanding the mechanism of oil accumulation in tissues other than seeds. Transcriptome analysis revealed the key members of gene families involved in fatty acid synthesis and TAG assembly in the caruncle. A transient expression assay of these selected genes resulted in a 20-fold increased TAG accumulation in leaves. CONCLUSIONS Castor caruncle utilizes an independent system to synthesize TAGs. Results provide the possibility of exploiting caruncle gene set to engineer oil production in non-seed tissues or microbes.
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Affiliation(s)
- Xia Wan
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062 People’s Republic of China
- CSIRO Agriculture & Food, PO Box 1700, Canberra, ACT 2601 Australia
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062 People’s Republic of China
- Key Laboratory of Oilseeds Processing, Ministry of Agriculture, Wuhan, 430062 People’s Republic of China
- Hubei Key Laboratory of Lipid Chemistry and Nutrition, Wuhan, 430062 People’s Republic of China
| | - Qing Liu
- CSIRO Agriculture & Food, PO Box 1700, Canberra, ACT 2601 Australia
| | - Bei Dong
- CSIRO Agriculture & Food, PO Box 1700, Canberra, ACT 2601 Australia
| | | | - Feng-Hong Huang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062 People’s Republic of China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062 People’s Republic of China
- Key Laboratory of Oilseeds Processing, Ministry of Agriculture, Wuhan, 430062 People’s Republic of China
- Hubei Key Laboratory of Lipid Chemistry and Nutrition, Wuhan, 430062 People’s Republic of China
| | | | - Xue-Rong Zhou
- CSIRO Agriculture & Food, PO Box 1700, Canberra, ACT 2601 Australia
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29
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Wang L, Jiang X, Wang L, Wang W, Fu C, Yan X, Geng X. A survey of transcriptome complexity using PacBio single-molecule real-time analysis combined with Illumina RNA sequencing for a better understanding of ricinoleic acid biosynthesis in Ricinus communis. BMC Genomics 2019; 20:456. [PMID: 31170917 PMCID: PMC6555039 DOI: 10.1186/s12864-019-5832-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 05/23/2019] [Indexed: 02/07/2023] Open
Abstract
Background Ricinus communis is a highly economically valuable oil crop plant from the spurge family, Euphorbiaceae. However, the available reference genomes are incomplete and to date studies on ricinoleic acid biosynthesis at the transcriptional level are limited. Results In this study, we combined PacBio single-molecule long read isoform and Illumina RNA sequencing to identify the alternative splicing (AS) events, novel isoforms, fusion genes, long non-coding RNAs (lncRNAs) and alternative polyadenylation (APA) sites to unveil the transcriptomic complexity of castor beans and identify critical genes related to ricinoleic acid biosynthesis. Here, we identified 11,285 AS-variants distributed in 21,448 novel genes and detected 520 fusion genes, 320 lncRNAs and 9511 (APA-sites). Furthermore, a total of 6067, 5983 and 4058 differentially expressed genes between developing beans of the R. communis lines 349 and 1115 with extremely different oil content were identified at 7, 14 and 21 days after flowering, respectively. Specifically, 14, 18 and 11 DEGs were annotated encoding key enzymes related to ricinoleic acid biosynthesis reflecting the higher castor oil content of 1115 compared than 349. Quantitative real-time RT-PCR further validated fifteen of these DEGs at three-time points. Conclusion Our results significantly improved the existed gene models of R. communis, and a putative model of key genes was built to show the differences between strains 349 and 1115, illustrating the molecular mechanism of castor oil biosynthesis. A multi-transcriptome database and candidate genes were provided to further improve the level of ricinoleic acid in transgenic crops. Electronic supplementary material The online version of this article (10.1186/s12864-019-5832-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lijun Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic, Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Xiaoling Jiang
- College of Life Science and Technology, Henan Institute of Science and Technology/Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, China
| | - Lei Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic, Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Wei Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic, Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Chunling Fu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic, Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China
| | - Xingchu Yan
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic, Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China.
| | - Xinxin Geng
- Applied Biotechnology Center, Wuhan University of Bioengineering, Wuhan, China.
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Ha J, Shim S, Lee T, Kang YJ, Hwang WJ, Jeong H, Laosatit K, Lee J, Kim SK, Satyawan D, Lestari P, Yoon MY, Kim MY, Chitikineni A, Tanya P, Somta P, Srinives P, Varshney RK, Lee S. Genome sequence of Jatropha curcas L., a non-edible biodiesel plant, provides a resource to improve seed-related traits. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:517-530. [PMID: 30059608 PMCID: PMC6335072 DOI: 10.1111/pbi.12995] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/26/2018] [Indexed: 05/02/2023]
Abstract
Jatropha curcas (physic nut), a non-edible oilseed crop, represents one of the most promising alternative energy sources due to its high seed oil content, rapid growth and adaptability to various environments. We report ~339 Mbp draft whole genome sequence of J. curcas var. Chai Nat using both the PacBio and Illumina sequencing platforms. We identified and categorized differentially expressed genes related to biosynthesis of lipid and toxic compound among four stages of seed development. Triacylglycerol (TAG), the major component of seed storage oil, is mainly synthesized by phospholipid:diacylglycerol acyltransferase in Jatropha, and continuous high expression of homologs of oleosin over seed development contributes to accumulation of high level of oil in kernels by preventing the breakdown of TAG. A physical cluster of genes for diterpenoid biosynthetic enzymes, including casbene synthases highly responsible for a toxic compound, phorbol ester, in seed cake, was syntenically highly conserved between Jatropha and castor bean. Transcriptomic analysis of female and male flowers revealed the up-regulation of a dozen family of TFs in female flower. Additionally, we constructed a robust species tree enabling estimation of divergence times among nine Jatropha species and five commercial crops in Malpighiales order. Our results will help researchers and breeders increase energy efficiency of this important oil seed crop by improving yield and oil content, and eliminating toxic compound in seed cake for animal feed.
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Affiliation(s)
- Jungmin Ha
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
- Plant Genomics and Breeding InstituteSeoul National UniversitySeoulKorea
| | - Sangrea Shim
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Taeyoung Lee
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Yang J. Kang
- Division of Applied Life Science (BK21 plus program) DepartmentGyeongsang National UniversityPMBBRCJinju‐siKorea
- Division of Life Science DepartmentGyeongsang National UniversityJinju‐siKorea
| | | | - Haneul Jeong
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Kularb Laosatit
- Department of AgronomyFaculty of Agriculture at Kamphaeng SaenKasetsart UniversityNakhon PathomThailand
| | - Jayern Lee
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Sue K. Kim
- Department of ChemistryCollege of Natural ScienceDankook UniversityCheonanSouth Korea
| | - Dani Satyawan
- Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD‐IAARD)BogorIndonesia
| | - Puji Lestari
- Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD‐IAARD)BogorIndonesia
| | - Min Y. Yoon
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Moon Y. Kim
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
- Plant Genomics and Breeding InstituteSeoul National UniversitySeoulKorea
| | - Annapurna Chitikineni
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadTelangana StateIndia
| | - Patcharin Tanya
- Department of AgronomyFaculty of Agriculture at Kamphaeng SaenKasetsart UniversityNakhon PathomThailand
| | - Prakit Somta
- Department of AgronomyFaculty of Agriculture at Kamphaeng SaenKasetsart UniversityNakhon PathomThailand
| | - Peerasak Srinives
- Department of AgronomyFaculty of Agriculture at Kamphaeng SaenKasetsart UniversityNakhon PathomThailand
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadTelangana StateIndia
| | - Suk‐Ha Lee
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
- Plant Genomics and Breeding InstituteSeoul National UniversitySeoulKorea
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Tian B, Lu T, Xu Y, Wang R, Chen G. Identification of genes associated with ricinoleic acid accumulation in Hiptage benghalensis via transcriptome analysis. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:16. [PMID: 30679955 DOI: 10.1186/s13068-019-1358-1352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/10/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND Ricinoleic acid is a high-value hydroxy fatty acid with broad industrial applications. Hiptage benghalensis seed oil contains a high amount of ricinoleic acid (~ 80%) and represents an emerging source of this unusual fatty acid. However, the mechanism of ricinoleic acid accumulation in H. benghalensis is yet to be explored at the molecular level, which hampers the exploration of its potential in ricinoleic acid production. RESULTS To explore the molecular mechanism of ricinoleic acid biosynthesis and regulation, H. benghalensis seeds were harvested at five developing stages (13, 16, 19, 22, and 25 days after pollination) for lipid analysis. The results revealed that the rapid accumulation of ricinoleic acid occurred at the early-mid-seed development stages (16-22 days after pollination). Subsequently, the gene transcription profiles of the developing seeds were characterized via a comprehensive transcriptome analysis with second-generation sequencing and single-molecule real-time sequencing. Differential expression patterns were identified in 12,555 transcripts, including 71 enzymes in lipid metabolic pathways, 246 putative transcription factors (TFs) and 124 long noncoding RNAs (lncRNAs). Twelve genes involved in diverse lipid metabolism pathways, including fatty acid biosynthesis and modification (hydroxylation), lipid traffic, triacylglycerol assembly, acyl editing and oil-body formation, displayed high expression levels and consistent expression patterns with ricinoleic acid accumulation in the developing seeds, suggesting their primary roles in ricinoleic acid production. Subsequent co-expression network analysis identified 57 TFs and 35 lncRNAs, which are putatively involved in the regulation of ricinoleic acid biosynthesis. The transcriptome data were further validated by analyzing the expression profiles of key enzyme-encoding genes, TFs and lncRNAs with quantitative real-time PCR. Finally, a network of genes associated with ricinoleic acid accumulation in H. benghalensis was established. CONCLUSIONS This study was the first step toward the understating of the molecular mechanisms of ricinoleic acid biosynthesis and oil accumulation in H. benghalensis seeds and identified a pool of novel genes regulating ricinoleic acid accumulation. The results set a foundation for developing H. benghalensis into a novel ricinoleic acid feedstock at the transcriptomic level and provided valuable candidate genes for improving ricinoleic acid production in other plants.
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Affiliation(s)
- Bo Tian
- 1Key Laboratory of Tropical Plant Resource and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223 China
| | - Tianquan Lu
- 1Key Laboratory of Tropical Plant Resource and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223 China
| | - Yang Xu
- 2Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5 Canada
| | - Ruling Wang
- 1Key Laboratory of Tropical Plant Resource and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223 China
| | - Guanqun Chen
- 2Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5 Canada
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Tian B, Lu T, Xu Y, Wang R, Chen G. Identification of genes associated with ricinoleic acid accumulation in Hiptage benghalensis via transcriptome analysis. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:16. [PMID: 30679955 PMCID: PMC6340187 DOI: 10.1186/s13068-019-1358-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/10/2019] [Indexed: 05/31/2023]
Abstract
BACKGROUND Ricinoleic acid is a high-value hydroxy fatty acid with broad industrial applications. Hiptage benghalensis seed oil contains a high amount of ricinoleic acid (~ 80%) and represents an emerging source of this unusual fatty acid. However, the mechanism of ricinoleic acid accumulation in H. benghalensis is yet to be explored at the molecular level, which hampers the exploration of its potential in ricinoleic acid production. RESULTS To explore the molecular mechanism of ricinoleic acid biosynthesis and regulation, H. benghalensis seeds were harvested at five developing stages (13, 16, 19, 22, and 25 days after pollination) for lipid analysis. The results revealed that the rapid accumulation of ricinoleic acid occurred at the early-mid-seed development stages (16-22 days after pollination). Subsequently, the gene transcription profiles of the developing seeds were characterized via a comprehensive transcriptome analysis with second-generation sequencing and single-molecule real-time sequencing. Differential expression patterns were identified in 12,555 transcripts, including 71 enzymes in lipid metabolic pathways, 246 putative transcription factors (TFs) and 124 long noncoding RNAs (lncRNAs). Twelve genes involved in diverse lipid metabolism pathways, including fatty acid biosynthesis and modification (hydroxylation), lipid traffic, triacylglycerol assembly, acyl editing and oil-body formation, displayed high expression levels and consistent expression patterns with ricinoleic acid accumulation in the developing seeds, suggesting their primary roles in ricinoleic acid production. Subsequent co-expression network analysis identified 57 TFs and 35 lncRNAs, which are putatively involved in the regulation of ricinoleic acid biosynthesis. The transcriptome data were further validated by analyzing the expression profiles of key enzyme-encoding genes, TFs and lncRNAs with quantitative real-time PCR. Finally, a network of genes associated with ricinoleic acid accumulation in H. benghalensis was established. CONCLUSIONS This study was the first step toward the understating of the molecular mechanisms of ricinoleic acid biosynthesis and oil accumulation in H. benghalensis seeds and identified a pool of novel genes regulating ricinoleic acid accumulation. The results set a foundation for developing H. benghalensis into a novel ricinoleic acid feedstock at the transcriptomic level and provided valuable candidate genes for improving ricinoleic acid production in other plants.
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Affiliation(s)
- Bo Tian
- Key Laboratory of Tropical Plant Resource and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223 China
| | - Tianquan Lu
- Key Laboratory of Tropical Plant Resource and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223 China
| | - Yang Xu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5 Canada
| | - Ruling Wang
- Key Laboratory of Tropical Plant Resource and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223 China
| | - Guanqun Chen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5 Canada
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Transcriptome Analysis Reveals Dynamic Fat Accumulation in the Walnut Kernel. Int J Genomics 2018; 2018:8931651. [PMID: 30622952 PMCID: PMC6304212 DOI: 10.1155/2018/8931651] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 09/09/2018] [Accepted: 09/16/2018] [Indexed: 01/02/2023] Open
Abstract
Walnut (Juglans regia L.) is an important woody oilseed species cultivated throughout the world. In this study, comparative transcript profiling was performed using high-throughput RNA sequencing technology at the following three stages of walnut fat synthesis in the “Lvling” walnut cultivar: the initial developmental stage (L1), the fast developing stage (L2), and the last developing stage (L3). A total of 68.18 GB of data were obtained on the three developmental stages, and 92% to 94% of clean data were able to be located to the reference genome. Further comparisons of the transcripts in the three libraries revealed that 724, 2027, and 4817 genes were differentially expressed between the L2 and L1 (L2vsL1), L3 and L2 (L3vsL2), and L3 and L1 (L3vsL1) samples, respectively. Through the GO gene enrichment analysis, differentially expressed genes (DEGs) in L2vsL1, L3vsL2, and L3vsL1 were enriched into 3, 0, and 2 functional categories, respectively. According to the KEGG enrichment analysis, DEGs in L2vsL1, L3vsL2, and L3vsL1 were annotated into 77, 110, and 3717 taxonomic metabolic pathways in the KEGG database, respectively. Next, we analyzed expression levels of genes related to fat synthesis. Our results indicated that ACCase, LACS, and FAD7 were the key genes related to fat synthesis. The high-throughput transcriptome sequencing of walnut in different developmental stages has greatly enriched the current genomic available resources. The comparison of DEGs under different developmental stages identified a wealth of candidate genes involved in fat synthesis, which will facilitate further genetic improvement and molecular studies of the walnut.
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Huang J, Hao X, Jin Y, Guo X, Shao Q, Kumar KS, Ahlawat YK, Harry DE, Joshi CP, Zheng Y. Temporal transcriptome profiling of developing seeds reveals a concerted gene regulation in relation to oil accumulation in Pongamia (Millettia pinnata). BMC PLANT BIOLOGY 2018; 18:140. [PMID: 29986660 PMCID: PMC6038193 DOI: 10.1186/s12870-018-1356-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 06/28/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Pongamia (Millettia pinnata syn. Pongamia pinnata), an oilseed legume species, is emerging as potential feedstock for sustainable biodiesel production. Breeding Pongamia for favorable traits in commercial application will rely on a comprehensive understanding of molecular mechanism regulating oil accumulation during its seed development. To date, only limited genomic or transcript sequences are available for Pongamia, while a temporal transcriptome profiling of developing seeds is still lacking in this species. RESULTS In this work, we conducted a time-series analysis of morphological and physiological characters, oil contents and compositions, as well as global gene expression profiles in developing Pongamia seeds. Firstly, three major developmental phases were characterized based on the combined evidences from embryonic shape, seed weight, seed moisture content, and seed color. Then, the gene expression levels at these three phases were quantified by RNA-Seq analyses with three biological replicates from each phase. Nearly 94% of unigenes were expressed at all three phases, whereas only less than 2% of unigenes were exclusively expressed at one of these phases. A total of 8881 differentially expressed genes (DEGs) were identified between phases. Furthermore, the qRT-PCR analyses for 10 DEGs involved in lipid metabolism demonstrated a good reliability of our RNA-Seq data in temporal gene expression profiling. We observed a dramatic increase in seed oil content from the embryogenesis phase to the early seed-filling phase, followed by a steady and moderate increase towards the maximum at the desiccation phase. We proposed that a highly active expression of most genes related to fatty acid (FA) and triacylglycerol (TAG) biosynthesis at the embryogenesis phase might trigger both the substantial oil accumulation and the membrane lipid synthesis for rapid cell proliferation at this phase, while a concerted reactivation of TAG synthesis-related genes at the desiccation phase might further promote storage lipid synthesis to achieve the maximum content of seed oils. CONCLUSIONS This study not only built a bridge between gene expression profiles and oil accumulation in developing seeds, but also laid a foundation for future attempts on genetic engineering of Pongamia varieties to acquire higher oil yield or improved oil properties for biofuel applications.
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Affiliation(s)
- Jianzi Huang
- Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 China
| | - Xuehong Hao
- Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 China
| | - Ye Jin
- Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 China
| | - Xiaohuan Guo
- Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 China
| | - Qing Shao
- Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 China
| | - Kavitha S. Kumar
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931 USA
| | - Yogesh K. Ahlawat
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931 USA
| | | | - Chandrashekhar P. Joshi
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931 USA
| | - Yizhi Zheng
- Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 China
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Waschburger E, Kulcheski FR, Veto NM, Margis R, Margis-Pinheiro M, Turchetto-Zolet AC. Genome-wide analysis of the Glycerol-3-Phosphate Acyltransferase (GPAT) gene family reveals the evolution and diversification of plant GPATs. Genet Mol Biol 2018; 41:355-370. [PMID: 29583156 PMCID: PMC5913721 DOI: 10.1590/1678-4685-gmb-2017-0076] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 08/01/2017] [Indexed: 01/05/2023] Open
Abstract
sn-Glycerol-3-phosphate 1-O-acyltransferase (GPAT) is an important enzyme that catalyzes the transfer of an acyl group from acyl-CoA or acyl-ACP to the sn-1 or sn-2 position of sn-glycerol-3-phosphate (G3P) to generate lysophosphatidic acids (LPAs). The functional studies of GPAT in plants demonstrated its importance in controlling storage and membrane lipid. Identifying genes encoding GPAT in a variety of plant species is crucial to understand their involvement in different metabolic pathways and physiological functions. Here, we performed genome-wide and evolutionary analyses of GPATs in plants. GPAT genes were identified in all algae and plants studied. The phylogenetic analysis showed that these genes group into three main clades. While clades I (GPAT9) and II (soluble GPAT) include GPATs from algae and plants, clade III (GPAT1-8) includes GPATs specific from plants that are involved in the biosynthesis of cutin or suberin. Gene organization and the expression pattern of GPATs in plants corroborate with clade formation in the phylogeny, suggesting that the evolutionary patterns is reflected in their functionality. Overall, our results provide important insights into the evolution of the plant GPATs and allowed us to explore the evolutionary mechanism underlying the functional diversification among these genes.
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Affiliation(s)
- Edgar Waschburger
- Graduação em Biotecnologia, Departamento de Biologia Molecular e Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Franceli Rodrigues Kulcheski
- Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal de Santa Catarina (UFSC), Florianópolis, SC, Brazil
| | - Nicole Moreira Veto
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Rogerio Margis
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Centro de Biotecnologia e Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Departamento de Biofísica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Marcia Margis-Pinheiro
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Andreia Carina Turchetto-Zolet
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
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Wang Y, Xu W, Chen Z, Han B, Haque ME, Liu A. Gene structure, expression pattern and interaction of Nuclear Factor-Y family in castor bean (Ricinus communis). PLANTA 2018; 247:559-572. [PMID: 29119268 DOI: 10.1007/s00425-017-2809-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/03/2017] [Indexed: 06/07/2023]
Abstract
Nuclear Factor-Y transcription factors, which function in regulating seed development (including storage reservoir accumulation) and responding to abiotic stresses, were identified and characterized in castor bean. Nuclear Factor-Y (NF-Y) transcription factors in plants contain three subunits (NF-YA, NF-YB and NF-YC), and function as a heterodimer or heterotrimer complex in regulating plant growth, development and response to stresses. Castor bean (Ricinus communis, Euphorbiaceae) one of the most economically important non-edible oilseed crops, able to grow in diverse soil conditions and displays high tolerance to abiotic stresses. Due to increasing demands for its seed oils, it is necessary to elucidate the molecular mechanism underlying the regulation of growth and development. Based on the available genome data, we identified 25 RcNF-Y members including six RcNF-YAs, 12 RcNF-YBs and seven RcNF-YCs, and characterized their gene structures. Yeast two-hybrid assays confirmed the protein-protein interactions among three subunits. Using transcriptomic data from different tissues, we found that six members were highly or specifically expressed in endosperms (in particular, two LEC1-type members RcNF-YB2 and RcNF-YB12), implying their involvement in regulating seed development and storage reservoir accumulation. Further, we investigated the expression changes of RcNF-Y members in two-week-old seedlings under drought, cold, hot and salt stresses. We found that the expression levels of 20 RcNF-Y members tested were changed and three RcNF-Y members might function in response to abiotic stresses. This study is the first reported on genomic characterization of NF-Y transcription factors in the family Euphorbiaceae. Our results provide the basis for improved understanding of how NF-Y genes function in the regulation of seed development and responses to abiotic stresses in both castor bean and other plants in this family.
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Affiliation(s)
- Yue Wang
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Wei Xu
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Zexi Chen
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bing Han
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mohammad E Haque
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Aizhong Liu
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
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Orona-Tamayo D, Valverde ME, Paredes-López O. Bioactive peptides from selected latin american food crops – A nutraceutical and molecular approach. Crit Rev Food Sci Nutr 2018; 59:1949-1975. [DOI: 10.1080/10408398.2018.1434480] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Domancar Orona-Tamayo
- Centro de Investigación y de Estudios Avanzados de Instituto Politécnico Nacional. Km. 9.6 Libramiento Norte Carretera Irapuato-León, Irapuato, Guanajuato, México, CP
| | - María Elena Valverde
- Centro de Investigación y de Estudios Avanzados de Instituto Politécnico Nacional. Km. 9.6 Libramiento Norte Carretera Irapuato-León, Irapuato, Guanajuato, México, CP
| | - Octavio Paredes-López
- Centro de Investigación y de Estudios Avanzados de Instituto Politécnico Nacional. Km. 9.6 Libramiento Norte Carretera Irapuato-León, Irapuato, Guanajuato, México, CP
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Wang B, Zhang Y, Haque ME, Xu W, Li F, Liu A. Transcriptomic analyses reveal complex and interconnected sucrose signaling cascades in developing seeds of castor bean. JOURNAL OF PLANT PHYSIOLOGY 2018; 221:1-10. [PMID: 29223877 DOI: 10.1016/j.jplph.2017.11.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 11/29/2017] [Accepted: 11/29/2017] [Indexed: 06/07/2023]
Abstract
Seeds are highly specific organs that strongly sink sucrose resources from leaf and stem tissues to trigger seed metabolism and development. In particular, for heterotrophic non-green seeds, the potential molecular mechanism underlying sucrose-driven seed development remains unanswered. Castor bean (Ricinus communis L.), a typical non-green seed, has been considered as a model plant for seed biology study in dicotyledonous plants due to its heterotrophic seeds with persistent endosperms. In the present study, the fast-developing castor bean seeds were treated with exogenous sucrose and mannitol for four hours. The global transcriptomic data were obtained by high-throughput RNA-seq technique, resulting in 468 differentially expressed genes (DGEs). Further analyses revealed that sucrose functioned as both metabolic substrates and signal molecules. Specifically, 73 DGEs involved in carbohydrate and nitrogen metabolism, 42 differentially expressed transcription factors, and 35 DGEs involved in diverse signaling pathways such as auxin, brassinosteroid, ethelyene, cytokinin, gibberellin, and calcium signals, were identified, suggesting that the sucrose signaling pathway might have complex and multi-connected cross-talks with other signals to regulate castor bean seed development. Taken together, this study provides novel data to improve understanding of the potential molecular mechanisms of sucrose in regulating non-green seed development and storage reservoir accumulation during seed development.
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Affiliation(s)
- Bin Wang
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Zhang
- Jiangxi Province Key Laboratory of Oil Crops Biology, Crops Research Institute of Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Mohammad Enamul Haque
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Xu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Fei Li
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Aizhong Liu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; College of Forestry, Southwest Forestry University, Kunming 650224, China.
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Zou Z, Huang Q, Xie G, Yang L. Genome-wide comparative analysis of papain-like cysteine protease family genes in castor bean and physic nut. Sci Rep 2018; 8:331. [PMID: 29321580 PMCID: PMC5762910 DOI: 10.1038/s41598-017-18760-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 12/18/2017] [Indexed: 11/09/2022] Open
Abstract
Papain-like cysteine proteases (PLCPs) are a class of proteolytic enzymes involved in many plant processes. Compared with the extensive research in Arabidopsis thaliana, little is known in castor bean (Ricinus communis) and physic nut (Jatropha curcas), two Euphorbiaceous plants without any recent whole-genome duplication. In this study, a total of 26 or 23 PLCP genes were identified from the genomes of castor bean and physic nut respectively, which can be divided into nine subfamilies based on the phylogenetic analysis: RD21, CEP, XCP, XBCP3, THI, SAG12, RD19, ALP and CTB. Although most of them harbor orthologs in Arabidopsis, several members in subfamilies RD21, CEP, XBCP3 and SAG12 form new groups or subgroups as observed in other species, suggesting specific gene loss occurred in Arabidopsis. Recent gene duplicates were also identified in these two species, but they are limited to the SAG12 subfamily and were all derived from local duplication. Expression profiling revealed diverse patterns of different family members over various tissues. Furthermore, the evolution characteristics of PLCP genes were also compared and discussed. Our findings provide a useful reference to characterize PLCP genes and investigate the family evolution in Euphorbiaceae and species beyond.
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Affiliation(s)
- Zhi Zou
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Baodaoxincun, Danzhou, 571737, Hainan Province, China.
| | - Qixing Huang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 570100, Hainan Province, China
| | - Guishui Xie
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Baodaoxincun, Danzhou, 571737, Hainan Province, China
| | - Lifu Yang
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Baodaoxincun, Danzhou, 571737, Hainan Province, China
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Aryal N, Lu C. A Phospholipase C-Like Protein From Ricinus communis Increases Hydroxy Fatty Acids Accumulation in Transgenic Seeds of Camelina sativa. FRONTIERS IN PLANT SCIENCE 2018; 9:1576. [PMID: 30443260 PMCID: PMC6221933 DOI: 10.3389/fpls.2018.01576] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 10/09/2018] [Indexed: 05/23/2023]
Abstract
There have been strong interests in producing unusual fatty acids in oilseed crops to provide renewable industrial feedstock. Results are so far largely disappointing since much lower amounts of such fatty acids accumulate in genetically engineered seeds than in their original natural sources. It has been suggested that the flux of unusual fatty acids through phosphatidylcholine (PC) represents a major bottleneck for high accumulation of such fatty acids in triacylglycerol (TAG). We show here that a phospholipase C-like protein (RcPLCL1) from castor bean, which accumulates nearly 90% of the hydroxylated ricinoleic acid in its seed TAG, increases the amount of hydroxy fatty acids (HFAs) when co-expresses with the fatty acid hydroxylase (RcFAH12) in transgenic seed of Camelina sativa. RcPLCL1 shows hydrolyzing activities on both PC and phosphatidylinositol substrates in our in vitro assay conditions. The PC-PLC activity of the RcPLCL1 may have increased the efficiency of HFA-PC to diacylglycerol conversion, which explains our observation of increased HFA contents in TAG concomitant with decreased HFA in the membrane lipid PC during seed development. Consequently, this may also alleviate the potential detrimental effect of HFA on germination of the engineered camelina seeds. Our results provide new knowledge that will help design effective strategies to engineer high levels of HFAs in transgenic oilseeds.
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41
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Ting MKY, She YM, Plaxton WC. Transcript profiling indicates a widespread role for bacterial-type phosphoenolpyruvate carboxylase in malate-accumulating sink tissues. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5857-5869. [PMID: 29240945 PMCID: PMC5854131 DOI: 10.1093/jxb/erx399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Phosphoenolpyruvate carboxylase (PEPC) is an important regulatory enzyme situated at a key branch point of central plant metabolism. Plant genomes encode several plant-type PEPC (PTPC) isozymes, along with a distantly related bacterial-type PEPC (BTPC). BTPC is expressed at high levels in developing castor oil seeds where it tightly interacts with co-expressed PTPC polypeptides to form unusual hetero-octameric Class-2 PEPC complexes that are desensitized to allosteric inhibition by L-malate. Analysis of RNA-Seq and microarray transcriptome datasets revealed two distinct patterns of tissue-specific BTPC expression in vascular plants. Species such as Arabidopsis thaliana, strawberry, rice, maize, and poplar mainly exhibited pollen- or floral-specific BTPC expression. By contrast, BTPC transcripts were relatively abundant in developing castor, cotton, and soybean seeds, cassava tubers, as well as immature tomato, cucumber, grape, and avocado fruit. Immunoreactive 118 kDa BTPC polypeptides were detected on immunoblots of cucumber and tomato fruit extracts. Co-immunoprecipitation established that as in castor, BTPCs physically interact with endogenous PTPCs to form Class-2 PEPC complexes in tomato and cucumber fruit. We hypothesize that Class-2 PEPCs simultaneously maintain rapid anaplerotic PEP carboxylation and respiratory CO2 refixation in diverse, biosynthetically active sinks that accumulate high malate levels.
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Affiliation(s)
- Michael K Y Ting
- Department of Biology, Queen’s University, Kingston, Ontario, Canada
| | - Yi-Min She
- Centre for Biologics Evaluation Biologics and Genetic Therapies Directorate, Health Canada, Ottawa, Ontario, Canada
| | - William C Plaxton
- Department of Biology, Queen’s University, Kingston, Ontario, Canada
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
- Correspondence:
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Fedosejevs ET, Liu LNC, Abergel M, She YM, Plaxton WC. Coimmunoprecipitation of reversibly glycosylated polypeptide with sucrose synthase from developing castor oilseeds. FEBS Lett 2017; 591:3872-3880. [PMID: 29110302 DOI: 10.1002/1873-3468.12893] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 10/23/2017] [Accepted: 10/24/2017] [Indexed: 11/09/2022]
Abstract
The sucrose synthase (SUS) interactome of developing castor oilseeds (COS; Ricinus communis) was assessed using coimmunoprecipitation (co-IP) with anti-(COS RcSUS1)-IgG followed by proteomic analysis. A 41-kDa polypeptide (p41) that coimmunoprecipitated with RcSUS1 from COS extracts was identified as reversibly glycosylated polypeptide-1 (RcRGP1) by LC-MS/MS and anti-RcRGP1 immunoblotting. Reciprocal Far-western immunodot blotting corroborated the specific interaction between RcSUS1 and RcRGP1. Co-IP using anti-(COS RcSUS1)-IgG and clarified extracts from other developing seeds as well as cluster (proteoid) roots of white lupin and Harsh Hakea consistently recovered 90 kDa SUS polypeptides along with p41/RGP as a SUS interactor. The results suggest that SUS interacts with RGP in diverse sink tissues to channel UDP-glucose derived from imported sucrose into hemicellulose and/or glycoprotein/glycolipid biosynthesis.
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Affiliation(s)
- Eric T Fedosejevs
- Department of Biology, Queen's University, Kingston, Ontario, Canada
| | - Leo N C Liu
- Department of Biology, Queen's University, Kingston, Ontario, Canada
| | - Megan Abergel
- Department of Biology, Queen's University, Kingston, Ontario, Canada
| | - Yi-Min She
- Centre for Biologics Evaluation, Biologics and Genetic Therapies Directorate, Health Canada, Ottawa, Ontario, Canada
| | - William C Plaxton
- Department of Biology, Queen's University, Kingston, Ontario, Canada
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
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43
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Aznar-Moreno JA, Durrett TP. Review: Metabolic engineering of unusual lipids in the synthetic biology era. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 263:126-131. [PMID: 28818368 DOI: 10.1016/j.plantsci.2017.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 06/06/2017] [Accepted: 07/07/2017] [Indexed: 05/07/2023]
Abstract
The plant kingdom produces a variety of fatty acid structures, many of which possess functional groups useful for industrial applications. The species that produce these unusual fatty acids are often not suitable for large scale commercial production. The ability to create genetically modified plants, together with emerging synthetic biology approaches, offers the potential to develop alternative oil seed crops capable of producing high levels of modified lipids. In some cases, by combining genes from different species, non-natural lipids with a targeted structure can be conceived. However, the expression of the biosynthetic enzymes responsible for the synthesis of unusual fatty acids typically results in poor accumulation of the desired product. An improved understanding of fatty acid flux from synthesis to storage revealed that specialized enzymes are needed to traffic unusual fatty acids. Co-expression of some of these additional enzymes has incrementally increased the levels of unusual fatty acids in transgenic seeds. Understanding how the introduced pathways interact with the endogenous pathways will be important for further enhancing the levels of unusual fatty acids in transgenic plants. Eliminating endogenous activities, as well as segregating the different pathways, represent strategies to further increase accumulation of unusual lipids.
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Affiliation(s)
- Jose A Aznar-Moreno
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - Timothy P Durrett
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA.
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44
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Wang ML, Dzievit M, Chen Z, Morris JB, Norris JE, Barkley NA, Tonnis B, Pederson GA, Yu J. Genetic diversity and population structure of castor (Ricinus communis L.) germplasm within the US collection assessed with EST-SSR markers. Genome 2017; 60:193-200. [PMID: 28094539 DOI: 10.1139/gen-2016-0116] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Castor is an important oilseed crop and although its oil is inedible, it has multiple industrial and pharmaceutical applications. The entire US castor germplasm collection was previously screened for oil content and fatty acid composition, but its genetic diversity and population structure has not been determined. Based on the screening results of oil content, fatty acid composition, and country origins, 574 accessions were selected and genotyped with 22 polymorphic EST-SSR markers. The results from cluster analysis, population structure, and principal component analysis were consistent, and partitioned accessions into four subpopulations. Although there were certain levels of admixtures among groups, these clusters and subpopulations aligned with geographic origins. Both divergent and redundant accessions were identified in this study. The US castor germplasm collection encompasses a moderately high level of genetic diversity (pairwise dissimilarity coefficient = 0.53). The results obtained here will be useful for choosing accessions as parents to make crosses in breeding programs and prioritizing accessions for regeneration to improve germplasm management. A subset of 230 accessions was selected and will be planted in the field for establishing a core collection of the US castor germplasm. Further evaluation of the US castor germplasm collection is also discussed.
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Affiliation(s)
- M L Wang
- a USDA-ARS, Plant Genetic Resources Conservation Unit, 1109 Experiment Street, Griffin, GA 30223, USA
| | - M Dzievit
- b Department of Agronomy, Iowa State University, 2014 Agronomy Hall, Ames, IA 50011, USA
| | - Z Chen
- c Department of Crop and Soil Sciences, University of Georgia, 1109 Experiment Street, Griffin, GA 30223, USA
| | - J B Morris
- a USDA-ARS, Plant Genetic Resources Conservation Unit, 1109 Experiment Street, Griffin, GA 30223, USA
| | - J E Norris
- d Emory University Hospital, Emory University, 1364 Clifton Road, Atlanta, GA 30322, USA
| | - N A Barkley
- a USDA-ARS, Plant Genetic Resources Conservation Unit, 1109 Experiment Street, Griffin, GA 30223, USA
| | - B Tonnis
- a USDA-ARS, Plant Genetic Resources Conservation Unit, 1109 Experiment Street, Griffin, GA 30223, USA
| | - G A Pederson
- a USDA-ARS, Plant Genetic Resources Conservation Unit, 1109 Experiment Street, Griffin, GA 30223, USA
| | - J Yu
- b Department of Agronomy, Iowa State University, 2014 Agronomy Hall, Ames, IA 50011, USA
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45
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Shah M, Teixeira FM, Soares EL, Soares AA, Carvalho PC, Domont GB, Thornburg RW, Nogueira FCS, Campos FAP. Time-course proteome analysis of developing extrafloral nectaries of Ricinus communis. Proteomics 2016; 16:629-33. [PMID: 26683443 DOI: 10.1002/pmic.201500292] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 10/30/2015] [Accepted: 11/24/2015] [Indexed: 11/05/2022]
Abstract
Floral and extrafloral nectaries are unique organs that secrete energy rich chemical components, but their contribution for nectar production is largely unknown. Here, we present the first comparative proteome dataset of four developmental stages of the extrafloral nectaries from castor plant (Ricinus communis), an important biofuel crop. Respectively, from stage I-IV, we identified 626, 613, 449 and 356 proteins, respectively, summing up 882 nonredundant proteins. Surprisingly, we identified two isoforms of the potent toxin ricin, indicating that ricin expression is not limited to seeds, but it may serve a general defense purpose for the castor plant. To date, this is the most complete dataset of proteins either from floral or extrafloral nectaries, thus contributing to lay the foundations for investigations on their ecological and evolutionary importance.
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Affiliation(s)
- Mohibullah Shah
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, Brazil
| | - Fabiano M Teixeira
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, Brazil
| | - Emanoella L Soares
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, Brazil
| | - Arlete A Soares
- Department of Biology, Federal University of Ceara, Fortaleza, Brazil
| | - Paulo C Carvalho
- Laboratory for Proteomics and Protein Engineering, Carlos Chagas Institute, Fiocruz, Paraná, Brazil
| | - Gilberto B Domont
- Proteomic Unit, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Robert W Thornburg
- Department of Biochemistry, Biophysics, & Molecular Biology, Iowa State University, Ames, IA, USA
| | - Fábio C S Nogueira
- Proteomic Unit, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Francisco A P Campos
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, Brazil
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46
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Payá-Milans M, Aznar-Moreno JA, Balbuena TS, Haslam RP, Gidda SK, Pérez-Hormaeche J, Mullen RT, Thelen JJ, Napier JA, Salas JJ, Garcés R, Martínez-Force E, Venegas-Calerón M. Sunflower HaGPAT9-1 is the predominant GPAT during seed development. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 252:42-52. [PMID: 27717477 DOI: 10.1016/j.plantsci.2016.07.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 07/04/2016] [Accepted: 07/07/2016] [Indexed: 05/25/2023]
Abstract
In oil crops, triacylglycerol biosynthesis is an important metabolic pathway in which glycerol-3-phosphate acyltransferase (GPAT) performs the first acylation step. Mass spectrometry analysis of developing sunflower (Helianthus annuus) seed membrane fractions identified an abundant GPAT, HaGPAT9 isoform 1, with a N-terminal peptide that possessed two phosphorylated residues with possible regulatory function. HaGPAT9-1 belongs to a broad eukaryotic GPAT family, similar to mammalian GPAT3, and it represents one of the two sunflower GPAT9 isoforms, sharing 90% identity with HaGPAT9-2. Both sunflower genes are expressed during seed development and in vegetative tissues, with HaGPAT9-1 transcripts accumulating at relatively higher levels than those for HaGPAT9-2. Green fluorescent protein tagging of HaGPAT9-1 confirmed its subcellular accumulation in the endoplasmic reticulum. Despite their overall sequence similarities, the two sunflower isoforms displayed significant differences in their enzymatic activities. For instance, HaGPAT9-1 possesses in vivo GPAT activity that rescues the lethal phenotype of the cmy228 yeast strain, while in vitro assays revealed a preference of HaGPAT9-1 for palmitoyl-, oleoyl- and linoleoyl-CoAs of one order of magnitude, with the highest increase in yield for oleoyl- and linoleoyl-CoAs. By contrast, no enzymatic activity could be detected for HaGPAT9-2, even though its over-expression modified the TAG profile of yeast.
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Affiliation(s)
- Miriam Payá-Milans
- Department of Biochemistry and Molecular Biology of Plant Products, Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide, 41013 Seville, Spain; Department of Entomology & Plant Pathology, University of Tennessee, Knoxville, TN 37996, United States
| | - Jose Antonio Aznar-Moreno
- Department of Biochemistry and Molecular Biology of Plant Products, Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide, 41013 Seville, Spain; Department of Biochemistry & Molecular Biophysics, Kansas State University, Manhattan, KS 66506, United States
| | - Tiago S Balbuena
- Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, United States; Department of Technology, São Paulo State University, Jaboticabal, São Paulo, Brazil
| | - Richard P Haslam
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
| | - Satinder K Gidda
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Javier Pérez-Hormaeche
- Department of Biochemistry and Molecular Biology of Plant Products, Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide, 41013 Seville, Spain
| | - Robert T Mullen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Jay J Thelen
- Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, United States
| | - Johnathan A Napier
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
| | - Joaquín J Salas
- Department of Biochemistry and Molecular Biology of Plant Products, Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide, 41013 Seville, Spain
| | - Rafael Garcés
- Department of Biochemistry and Molecular Biology of Plant Products, Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide, 41013 Seville, Spain
| | - Enrique Martínez-Force
- Department of Biochemistry and Molecular Biology of Plant Products, Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide, 41013 Seville, Spain
| | - Mónica Venegas-Calerón
- Department of Biochemistry and Molecular Biology of Plant Products, Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide, 41013 Seville, Spain.
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47
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Niederhuth CE, Bewick AJ, Ji L, Alabady MS, Kim KD, Li Q, Rohr NA, Rambani A, Burke JM, Udall JA, Egesi C, Schmutz J, Grimwood J, Jackson SA, Springer NM, Schmitz RJ. Widespread natural variation of DNA methylation within angiosperms. Genome Biol 2016; 17:194. [PMID: 27671052 DOI: 10.1101/045880] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/09/2016] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND DNA methylation is an important feature of plant epigenomes, involved in the formation of heterochromatin and affecting gene expression. Extensive variation of DNA methylation patterns within a species has been uncovered from studies of natural variation. However, the extent to which DNA methylation varies between flowering plant species is still unclear. To understand the variation in genomic patterning of DNA methylation across flowering plant species, we compared single base resolution DNA methylomes of 34 diverse angiosperm species. RESULTS By analyzing whole-genome bisulfite sequencing data in a phylogenetic context, it becomes clear that there is extensive variation throughout angiosperms in gene body DNA methylation, euchromatic silencing of transposons and repeats, as well as silencing of heterochromatic transposons. The Brassicaceae have reduced CHG methylation levels and also reduced or loss of CG gene body methylation. The Poaceae are characterized by a lack or reduction of heterochromatic CHH methylation and enrichment of CHH methylation in genic regions. Furthermore, low levels of CHH methylation are observed in a number of species, especially in clonally propagated species. CONCLUSIONS These results reveal the extent of variation in DNA methylation in angiosperms and show that DNA methylation patterns are broadly a reflection of the evolutionary and life histories of plant species.
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Affiliation(s)
- Chad E Niederhuth
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, USA
| | - Adam J Bewick
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, USA
| | - Lexiang Ji
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - Magdy S Alabady
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Kyung Do Kim
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
| | - Qing Li
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Nicholas A Rohr
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, USA
| | - Aditi Rambani
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT, 84602, USA
| | - John M Burke
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Joshua A Udall
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Chiedozie Egesi
- National Root Crops Research Institute (NRCRI), Umudike, Km 8 Ikot Ekpene Road, PMB 7006, Umuahia, 440001, Nigeria
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
| | - Nathan M Springer
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT, 84602, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, USA.
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48
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Niederhuth CE, Bewick AJ, Ji L, Alabady MS, Kim KD, Li Q, Rohr NA, Rambani A, Burke JM, Udall JA, Egesi C, Schmutz J, Grimwood J, Jackson SA, Springer NM, Schmitz RJ. Widespread natural variation of DNA methylation within angiosperms. Genome Biol 2016; 17:194. [PMID: 27671052 PMCID: PMC5037628 DOI: 10.1186/s13059-016-1059-0] [Citation(s) in RCA: 329] [Impact Index Per Article: 41.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/09/2016] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND DNA methylation is an important feature of plant epigenomes, involved in the formation of heterochromatin and affecting gene expression. Extensive variation of DNA methylation patterns within a species has been uncovered from studies of natural variation. However, the extent to which DNA methylation varies between flowering plant species is still unclear. To understand the variation in genomic patterning of DNA methylation across flowering plant species, we compared single base resolution DNA methylomes of 34 diverse angiosperm species. RESULTS By analyzing whole-genome bisulfite sequencing data in a phylogenetic context, it becomes clear that there is extensive variation throughout angiosperms in gene body DNA methylation, euchromatic silencing of transposons and repeats, as well as silencing of heterochromatic transposons. The Brassicaceae have reduced CHG methylation levels and also reduced or loss of CG gene body methylation. The Poaceae are characterized by a lack or reduction of heterochromatic CHH methylation and enrichment of CHH methylation in genic regions. Furthermore, low levels of CHH methylation are observed in a number of species, especially in clonally propagated species. CONCLUSIONS These results reveal the extent of variation in DNA methylation in angiosperms and show that DNA methylation patterns are broadly a reflection of the evolutionary and life histories of plant species.
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Affiliation(s)
- Chad E Niederhuth
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, USA
| | - Adam J Bewick
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, USA
| | - Lexiang Ji
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - Magdy S Alabady
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Kyung Do Kim
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
| | - Qing Li
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Nicholas A Rohr
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, USA
| | - Aditi Rambani
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT, 84602, USA
| | - John M Burke
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Joshua A Udall
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Chiedozie Egesi
- National Root Crops Research Institute (NRCRI), Umudike, Km 8 Ikot Ekpene Road, PMB 7006, Umuahia, 440001, Nigeria
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
| | - Nathan M Springer
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT, 84602, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, USA.
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49
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The calcium-dependent protein kinase RcCDPK2 phosphorylates sucrose synthase at Ser11 in developing castor oil seeds. Biochem J 2016; 473:3667-3682. [PMID: 27512054 DOI: 10.1042/bcj20160531] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 08/10/2016] [Indexed: 12/11/2022]
Abstract
Imported sucrose is cleaved by sucrose synthase (SUS) as a critical initial reaction in the biosynthesis of storage end-products by developing seeds. Although SUS is phosphorylated at a conserved seryl residue by an apparent CDPK (Ca2+-dependent protein kinase) in diverse plant tissues, the functions and mechanistic details of this process remain obscure. Thus, the native CDPK that phosphorylates RcSUS1 (Ricinus communis SUS1) at Ser11 in developing COS (castor oil seeds) was highly purified and identified as RcCDPK2 by MS/MS. Purified RcSUS1-K (-kinase) and heterologously expressed RcCDPK2 catalyzed Ca2+-dependent Ser11 phosphorylation of RcSUS1 and its corresponding dephosphopeptide, while exhibiting a high affinity for free Ca2+ ions [K0.5(Ca2+) < 0.4 µM]. RcSUS1-K activity, RcCDPK2 expression, and RcSUS1 Ser11 phosphorylation peaked during early COS development and then declined in parallel. The elimination of sucrose import via fruit excision triggered RcSUS1 dephosphorylation but did not alter RcSUS1-K activity, suggesting a link between sucrose signaling and posttranslational RcCDPK2 control. Both RcCDPK2-mCherry and RcSUS1-EYFP co-localized throughout the cytosol when transiently co-expressed in tobacco suspension cells, although RcCDPK2-mCherry was also partially localized to the nucleus. Subcellular fractionation revealed that ∼20% of RcSUS1-K activity associates with microsomal membranes in developing COS, as does RcSUS1. In contrast with RcCDPK1, which catalyzes inhibitory phosphorylation of COS bacterial-type phosphoenolpyruvate carboxylase at Ser451, RcCDPK2 exhibited broad substrate specificity, a wide pH-activity profile centered at pH 8.5, and insensitivity to metabolite effectors or thiol redox status. Our combined results indicate a possible link between cytosolic Ca2+-signaling and the control of photosynthate partitioning during COS development.
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50
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Singer SD, Chen G, Mietkiewska E, Tomasi P, Jayawardhane K, Dyer JM, Weselake RJ. Arabidopsis GPAT9 contributes to synthesis of intracellular glycerolipids but not surface lipids. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:4627-38. [PMID: 27325892 PMCID: PMC4973736 DOI: 10.1093/jxb/erw242] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE (GPAT) genes encode enzymes involved in glycerolipid biosynthesis in plants. Ten GPAT homologues have been identified in Arabidopsis. GPATs 4-8 have been shown to be involved in the production of extracellular lipid barrier polyesters. Recently, GPAT9 was reported to be essential for triacylglycerol (TAG) biosynthesis in developing Arabidopsis seeds. The enzymatic properties and possible functions of GPAT9 in surface lipid, polar lipid and TAG biosynthesis in non-seed organs, however, have not been investigated. Here we show that Arabidopsis GPAT9 exhibits sn-1 acyltransferase activity with high specificity for acyl-coenzyme A, thus providing further evidence that this GPAT is involved in storage lipid biosynthesis. We also confirm a role for GPAT9 in seed oil biosynthesis and further demonstrate that GPAT9 contributes to the biosynthesis of both polar lipids and TAG in developing leaves, as well as lipid droplet production in developing pollen grains. Conversely, alteration of constitutive GPAT9 expression had no obvious effects on surface lipid biosynthesis. Taken together, these studies expand our understanding of GPAT9 function to include modulation of several different intracellular glycerolipid pools in plant cells.
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Affiliation(s)
- Stacy D Singer
- Agricultural Lipid Biotechnology Program, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
| | - Guanqun Chen
- Agricultural Lipid Biotechnology Program, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
| | - Elzbieta Mietkiewska
- Agricultural Lipid Biotechnology Program, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
| | - Pernell Tomasi
- USDA-ARS, US Arid-Land Agricultural Research Center, 21881 North Cardon Lane, Maricopa, AZ 85138, USA
| | - Kethmi Jayawardhane
- Agricultural Lipid Biotechnology Program, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
| | - John M Dyer
- USDA-ARS, US Arid-Land Agricultural Research Center, 21881 North Cardon Lane, Maricopa, AZ 85138, USA
| | - Randall J Weselake
- Agricultural Lipid Biotechnology Program, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
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